http://wiki.docking.org/api.php?action=feedcontributions&user=Matthew+O%27Meara&feedformat=atomDISI - User contributions [en]2024-03-19T03:45:45ZUser contributionsMediaWiki 1.39.1http://wiki.docking.org/index.php?title=AMSOL&diff=13739AMSOL2021-10-30T13:56:59Z<p>Matthew O'Meara: give command to apply intcar.f patch for amsol7.1</p>
<hr />
<div>From the [http://comp.chem.umn.edu/amsol/ AMSOL Web Site]:<br />
<br />
AMSOL is a semiempirical quantum chemistry program that includes the MINDO/3, MNDO, AM1, and PM3 gas-phase Hamiltonians, the CM1A, CM1P, CM2/AM1, CM2/PM3, CM3/AM1, and CM3/PM3 charge models for calculating partial atomic charges, the SM1 - SM5.42R solvation models for calculating free energies of solvation in water, the SM4 solvation model for calculating free energies of solvation in alkanes, and the SM5.42R, SM5.4, SM5.2R, and SM5.0R solvation models for calculating free energies of solvation in any organic solvent. Most of the solvation models are based on the AM1 and/or PM3 Hamiltonians; the SM5.2R model is also available with the MNDO Hamiltonian. AMSOL can also accept user-specified specific reaction parameters. All solvation models that are denoted with an "R" in their name are for rigid-solute calculations and were designed to utilize accurate gas-phase geometries to predict solvation free energies. For all other models, geometry optimization is possible in both the gas phase and solution. For SM5.4 models analytic derivatives are available for geometry optimization.<br />
<br />
* AMSOL is used by [[ZINC]].<br />
<br />
==Installation==<br />
Go here: https://secure.nouvant.com/umn/technology/z05201/license/153/agreements/new<br />
Install this on sgehead: ~]# <br />
yum install compat-gcc-34-g77.x86_64<br />
Fill in the license information. <br /><br />
Download the gzip file.<br /><br />
Unzip it.<br /><br />
Change into the directory and run the amsol.compile file.<br /><br />
<br />
== Compiling ==<br />
If you're on a newer Linux machine and get errors compiling, then you may need to apply the following changes to '''new/amsol.f''':<br />
<pre><br />
26,27c26,27<br />
< OPEN(19,NAME='fort.19') BJL1003<br />
< OPEN(20,NAME='fort.20') BJL1003<br />
---<br />
> OPEN(19,file='fort.19') BJL1003<br />
> OPEN(20,file='fort.20') BJL1003<br />
</pre><br />
<br />
If you don't know what that means, then just find the file '''new/amsol.f''' and find lines 26 and 27 which should be<br />
OPEN(19,NAME='fort.19') BJL1003<br />
OPEN(20,NAME='fort.20') BJL1003<br />
and replace that with<br />
OPEN(19,file='fort.19') BJL1003<br />
OPEN(20,file='fort.20') BJL1003<br />
<br />
===Patches===<br />
For using Amsol7.1 with dock3.7, we distribute a patch: <br />
$DOCKBASE/ligand/amsol/patches/amsol7.1_port_intcar.f.diff<br />
<br />
This patch resolve an issue with linear molecules. <br />
<br />
Consider applying this patch and then recompile amsol7.1.<br />
<pre><br />
patch port/intcar.f ${DOCKBASE}/ligand/amsol/patches/amsol7.1_port_intcar.f.diff<br />
</pre><br />
<br />
===Large Molecules===<br />
By default AMSOL limits the number of heavy atoms to 60 and the number of light atoms (i.e. hydrogens) to 60. To increase the limit,<br />
in '''include/SIZES.i''' edit the following line<br />
<br />
PARAMETER (MAXHEV=60, MAXLIT=60, NCHAIN=60, NRELAX=25) DL0397<br />
<br />
to, for example,<br />
<br />
PARAMETER (MAXHEV=80, MAXLIT=110, NCHAIN=60, NRELAX=25) DL0397<br />
<br />
and recompile by running make in the base directory<br />
<br />
make<br />
<br />
<br />
<br />
<br />
[[Category:Solvation]]<br />
[[Category:Software]]<br />
[[Category:Freecom]]</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=How_to_do_parameter_scanning&diff=13682How to do parameter scanning2021-09-21T20:04:04Z<p>Matthew O'Meara: add dollar signs to shell variables</p>
<hr />
<div>== Manually Generating ES/LD Combinations ==<br />
<br />
written by Reed Stein, updated 12/2019 so users can specify different low dielectric and ligand desolvation sphere radii<br />
<br />
To generate different sized low dielectric and ligand desolvation thin sphere combinations, you must first run blastermaster on your protein/ligand of interest. Once this is finished, make a new directory. Change into the new directory<br />
and run the following command:<br />
<br />
python ~rstein/zzz.scripts/DOCK_prep_scripts/new_0001_generate_ES_LD_generation.py -p ${FULL_ORIGINAL_BLASTERMASTER_PATH}<br />
<br />
The full path to your original blastermaster path is the only required argument. However, you can modify other default values including:<br />
1) Radius of low dielectric spheres you want to run: use the -es flag. <br />
Default radius for electrostatic spheres is [1.0, 1.3, 1.5, 1.7, 1.9]<br />
2) Radius of ligand desolvation spheres you want to run: use the -ld flag. <br />
Default radius for ligand desolvation spheres is [0.1, 0.2, 0.3, 0.4, 0.5]<br />
3) DMS density: use the -d flag. Default is 10.0 to ensure that the surface is sufficiently coated with spheres when using <br />
a smaller sphere radii (typically <0.5 Å). This can be reduced to 1.0 if only larger sphere radii are used.<br />
4) Distance from crystallographic ligand: use the -xd flag. Default is 2 Å.<br />
<br />
If you wanted to change all, you could use:<br />
<br />
python ~rstein/zzz.scripts/DOCK_prep_scripts/new_0001_generate_ES_LD_generation.py -p ${FULL_ORIGINAL_BLASTERMASTER_PATH} <br />
-es 1.1 1.2 1.3 -ld 0.1 0.3 -d 10 -xd 4<br />
<br />
This script will submit ligand desolvation jobs to the queue. This should take 15-30 minutes. Once finished, check your spheres and grids by following the steps here:<br />
<br />
http://wiki.docking.org/index.php/Protein_Target_Preparation_Updated<br />
<br />
Then run the following script to combine the ES/LD grids in all combinations:<br />
<br />
python ~rstein/zzz.scripts/DOCK_prep_scripts/new_0002_combine_es_ld_grids_into_combos.py -p ${FULL_ORIGINAL_BLASTERMASTER_PATH}<br />
<br />
This will create a new directory called "combo_directories" with docking-ready directories inside. The directories will have the name format "es_{ES_sphere_radius}_ld_{LD_sphere_radius}". "def" refers to grids taken from your ${FULL_ORIGINAL_BLASTERMASTER_PATH} directory.<br />
<br />
These directories are now ready for docking.<br />
<br />
== Blastermaster Parameter Scanning == <br />
<br />
Written by Jiankun Lyu, 2017/01/18<br />
<br />
4/16/2019 - this needs to be updated and will result in discontinuous thin spheres at low radii! <br />
Use the tutorial above instead. Or use this link to run blastermaster manually:<br />
<br />
http://wiki.docking.org/index.php/Using_thin_spheres_in_DOCK3.7<br />
<br />
<br />
The hierarchy of the directories:<br />
<br />
thin_spheres_parameter_scanning----- std_dockprep <br />
|<br />
|------ dockfiles<br />
| | <br />
| |----- working<br />
| |<br />
| ------ rec.pdb, xtal-lig.pdb, INDOCK and other files generated balstermaster.py<br />
|<br />
------- script ------ dockprep_thin_spheres_in_batches.csh<br />
|<br />
|------ submit_dockprep_thin_spheres.csh<br />
|<br />
|------ dockprep_thin_spheres.csh<br />
|<br />
|------ lig-decoy_enrichment.csh<br />
|<br />
|------ combineScoresAndPoses.csh<br />
|<br />
|------ AUCplot_of-lig-decoys.csh<br />
|<br />
|------ mk_matrix_logAUC.py<br />
|<br />
|------ sph_lib.py<br />
|<br />
|------ pdb_lib.py<br />
|<br />
------- close_sph.py<br />
<br />
1) Make those directories above.<br />
mkdir thin_spheres_parameter_scanning<br />
cd thin_spheres_parameter_scanning<br />
mkdir std_dockprep<br />
mkdir script<br />
<br />
2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles<br />
<br />
3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory<br />
cd script<br />
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py<br />
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py<br />
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py<br />
<br />
4) Copy scripts from my path, and modify as necessary.<br />
<br />
cd script<br />
<br />
cp /mnt/nfs/ex5/work/jklyu/large_scale_docking/DRD2/struct_20180322/A122I_add_polarH_mini_HID/thin_spheres_parameter_scanning/scripts/*dockprep* .<br />
<br />
cp /mnt/nfs/reshwork/jklyu/D2R/scripts/lig-decoy_enrichment_submit.csh .<br />
cp /mnt/nfs/reshwork/jklyu/D2R/scripts/combineScoresAndPoses.csh .<br />
cp /mnt/nfs/reshwork/jklyu/D2R/scripts/mk_matrix_logAUC.py .<br />
<br />
<br />
5) Run parameter scanning.<br />
cd ../ # go back to thin_spheres_parameter_scanning folder<br />
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep<br />
<br />
<br />
Note:- you can edit dockprep_thin_spheres_in_batches.csh to include more CPUs in Job Bound<br />
<br />
6) make the following subfolders<br />
<br />
mkdir ligands-decoys<br />
cd ligands-decoys<br />
mkdir ligands<br />
mkdir decoys<br />
<br />
now copy your decoys.db2.gz to decoys<br />
now copy your ligands.db2.gz to ligands<br />
now copy decoys.smi to the folder<br />
now copy ligands.smi to the folder<br />
<br />
7) Submit DOCK and enrichment calculation.<br />
csh /path/to/script/lig-decoy_enrichment.csh<br />
<br />
8) Combine and analyze the docking results.<br />
csh /path/to/script/combineScoresAndPoses.csh #1st change the path inside the script to your own dir<br />
csh /path/to/script/AUCplot_of-lig-decoys.csh #1st change the path inside the script to your own dir<br />
<br />
9) Visualize the logAUC by heatmap.<br />
python /path/to/script/mk_matrix_logAUC.py</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Google_sheets_hit_picking&diff=12983Google sheets hit picking2020-10-05T17:06:08Z<p>Matthew O'Meara: </p>
<hr />
<div>To display substance 2D structure by smiles<br />
<ol><br />
<li> Put the smiles in column e.g. B2-B100 and then put this formula in the adjacent column</li><br />
<br />
=IMAGE(CONCATENATE("http://zinc15.docking.org/apps/mol/draw.png?smiles=", ENCODEURL(B59)))<br />
<br />
<li> I sometimes have issues with the compounds loading, so it may be useful to save them once they load. Copy column and paste in adjacent column and select "by value" from the drop-down list</li><br />
</ol><br />
<br />
To Displaying substance 2D structure from ZINC_ID<br />
<ol><br />
<li>'''Sort zinc_ids numerically'''. This is really important because ZINC returns the values sorted numerically and if they aren't pre-sorted results won't match up with the right compound.<br />
<ol><br />
<li>Put zinc_ids in a column, e.g. B2-B100'</li><br />
<li>If you try to sort them directly, it will sort them lexigraphically, eg. put ZINC100 before ZINC34. So extract the zinc number from the zinc id by making a column 'ZINC_Number" by putting in cell C2</li><br />
<br />
=VALUE(SUBSTITUTE(B2, "ZINC", ""))<br />
<br />
<li>sort sort the cells by the ZINC_Number column by selecting the whole sheet and then data --> sort range... --> ZINC_Number</li><br />
</li><br />
</ol><br />
<li>To depict the molecules copy and paste the following in each cells in new column. E.g. put this in cell D2 to depict the molecule in B2</li><br />
<br />
=IMAGE(CONCATENATE("http://zinc15.docking.org/substances/", B2, "-small.png"))<br />
<br />
<li>Use IMPORTDATA to populate additional columns of interest in the header of the next columns. It looks like it can only load 3 columns at a time, so for example put ZINC_Number in column B and to retrieve data from ZINC into columns E-H, make those columns empty an put into cell E1 the IMPORTDATA function call</li><br />
<br />
Put in cell E1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=zinc_id smiles mol_formula logp"))<br />
<br />
Then to fill in I-K:<br />
<br />
Put in cell I1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=mwt num_chiral_centers reactivity"))<br />
<br />
And to fill in L-M:<br />
<br />
Put in cell L1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=predicted_gene_names purchasability supplier_codes"))<br />
<br />
To figure out what column Look up additional columns of interest here http://zinc15.docking.org/substances/help/. As a sanity check include the zinc_id in the output column and verify that it corresponds with the input column</li><br />
</ol></div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Google_sheets_hit_picking&diff=12982Google sheets hit picking2020-10-05T17:01:23Z<p>Matthew O'Meara: </p>
<hr />
<div>To display substance 2D structure by smiles<br />
<ol><br />
<li> Put the smiles in column e.g. B2-B100 and then put this formula in the adjacent column</li><br />
<br />
=IMAGE(CONCATENATE("http://zinc15.docking.org/apps/mol/draw.png?smiles=", ENCODEURL(B59)))<br />
<br />
<li> I sometimes have issues with the compounds loading, so it may be useful to save them once they load. Copy column and paste in adjacent column and select "by value" from the drop-down list</li><br />
</ol><br />
<br />
To Displaying substance 2D structure from ZINC_ID<br />
<ol><br />
<li>'''Sort zinc_ids numerically'''. This is really important because ZINC returns the values sorted numerically and if they aren't pre-sorted results won't match up with the right compound.<br />
<ol><br />
<li>Put zinc_ids in a column, e.g. B2-B100'</li><br />
<li>If you try to sort them directly, it will sort them lexigraphically, eg. put ZINC100 before ZINC34. So extract the zinc number from the zinc id by making a column 'ZINC_Number" by putting in cell C2</li><br />
<br />
=VALUE(SUBSTITUTE(B2, "ZINC", ""))<br />
<br />
<li>sort sort the cells by the ZINC_Number column by selecting the whole sheet and then data --> sort range... --> ZINC_Number</li><br />
</li><br />
</ol><br />
<li>To depict the molecules copy and paste the following in each cells in new column. E.g. put this in cell D2 to depict the molecule in B2</li><br />
<br />
=IMAGE(CONCATENATE("http://zinc15.docking.org/substances/", B2, "-small.png"))<br />
<br />
<li>Use IMPORTDATA to populate additional columns of interest in the header of the next columns. It looks like it can only load 3 columns at a time, so for example put ZINC_Number in column B and to retrieve data from ZINC into columns E-H, make those columns empty an put into cell E1 the IMPORTDATA function call:<br />
<br />
Put in cell E1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=zinc_id smiles mol_formula logp"))<br />
<br />
Then to fill in I-K:<br />
<br />
Put in cell I1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=mwt num_chiral_centers reactivity"))<br />
<br />
And to fill in L-M:<br />
<br />
Put in cell L1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=predicted_gene_names purchasability supplier_codes"))<br />
</ol><br />
<br />
To figure out what column Look up additional columns of interest here http://zinc15.docking.org/substances/help/. As a sanity check include the zinc_id in the output column and verify that it corresponds with the input column</li></div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=DOCK_3.7_tutorial_(Anat)&diff=12865DOCK 3.7 tutorial (Anat)2020-08-19T16:46:11Z<p>Matthew O'Meara: fix typo art -> tart</p>
<hr />
<div>==DOCK 3.7==<br />
<br />
source /nfs/soft/dock/DOCK-3.7-beta3/env.csh<br />
source ~/.cshrc_dock37 (my home directory)<br />
*“Up directory” refers to the main directory that contains the ‘dockfiles’ and ‘working’ directories.<br />
<br />
=== protein prep ===<br />
blastermaster.py --addhOptions=" -HIS -FLIPs " -v <br />
'$DOCKBASE/proteins/blastermaster/blastermaster.py'<br />
* Use -v flag (verbose) to see what’s happening.<br />
blastermaster.py --addNOhydrogensflag <br />
* The flag "addNOhydrogensflag" is for when you want to keep the hydrogens.<br />
<br />
=== ligand prep ===<br />
build_smiles_ligand.sh '$DOCKBASE/ligand/generate/build_smiles_ligand.sh'<br />
build_covalent_lib.csh '$DOCKBASE/ligand/generate/build_covalent_lib.csh'<br />
combine_gz_files.sh '$DOCKBASE/ligand/generate/combine_gz_files.sh'<br />
<br />
* Make sure that there are no ^M in the smiles input file - use dos2unix [file name] command remove them.<br />
<br />
===Set docking directories===<br />
* This is for running a virtual screen on a ZINC subset, thing can be in different paths. <br />
* Input file should contain a db2 file on each line with full path. <br />
* This file may be downloaded from the zinc webpage: '[http://zinc15.docking.org/tranches/home http://zinc15.docking.org/tranches/home]'<br />
<br />
setup_db2_zinc15_file.py '$DOCKBASE/docking/setup/setup_db2_zinc15_file.py'<br />
<br />
The commands will be:<br />
mkdir Frag <br />
* Make this directory in the top directory that also has the dockfiles and working directories.<br />
cp INDOCK database_index Frag/<br />
cd Frag/<br />
ln -s ../dockfiles/ .<br />
<br />
python ${DOCKBASE}/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /path/to/ZINC-downloader-3D-db2.gz.database_index 1000 count<br />
<br />
See the this page: [[Trent_scripts]]<br />
<br />
* prepare databases for docking if ligand databases are all in the same directory (path). <br />
setup_db2.csh '$DOCKBASE/docking/setup/setup_db2.csh'<br />
setup_db2_lots.py '$DOCKBASE/docking/setup/setup_db2_lots.py'<br />
<br />
setup_db2.csh /path/to/ligands/lig_db2/<br />
* run it from the up directory that contains the ‘working’ and ‘dockfiles’ directory.<br />
* tip: use FULL path to the db files (and not ../../etc)<br />
<br />
=== submit docking calculations ===<br />
submit.csh '$DOCKBASE/docking/submit/submit.csh'<br />
* For small ligand libraries you prepared yourself, run it from the up directory, that now has the ‘dirlist’ file, and ‘working’ and ‘dockfiles’ directories.<br />
* For virtual screens of Zinc libraries - run the command from the library that has all the tranches (i.e., the ‘Frags’ library.. where you ran the setup_db2_zinc15_file.py script).<br />
<br />
=== for combining docking results. ===<br />
extract_all.py '$DOCKBASE/analysis/extract_all.py'<br />
getposes.py '$DOCKBASE/analysis/getposes.py'<br />
* to write out more then 1 pose per molecue, use the --topx=?? flag.<br />
* run it from the up directory<br />
<br />
=== for enrichment ===<br />
enrich.py '$DOCKBASE/analysis/enrich.py'<br />
plots.py '$DOCKBASE/analysis/plots.py'<br />
<br />
=== Tarting a residue in DOCK3.7 ===<br />
<br />
[[DOCK_3.7_tart]]<br />
<br />
Tarting refers to the polarization of specific atoms in the protein receptor to modify (enhance/decrease) ligand preferences for specific parts of the binding site. Generally one would redefine the partial charges distribution of a specific amino acid, and then use this modified residue when calculating the electrostatic potential for the receptor. Below is a step by step example:<br />
Let's say you ran docking against RSK2, so you have a docking directory that looks like: rec.pdb, xtal-lig.pdb, dockfiles, working, INDOCK<br />
Make a new dir e.g. RSK2-tart, and copy some input files into it:<br />
mkdir RSK2-tart<br />
cp RSK2/rec.pdb RSK2/xtal-lig.pdb RSK2-tart<br />
mkdir -p RSK2-tart/working<br />
cp RSK2/working/rec.crg.pdb RSK2-tart/working<br />
cp RSK2/working/prot.table.ambcrg.ambH RSK2/working/amb.crg.oxt RSK2-tart<br />
* the prot.table.amb.crg.ambH and amb.crg.oxt files should be in the up directory and NOT in the ‘working’ directory.<br />
Now edit the files to represent your tweaked polarization. Let's say we want to polarize the backbone of MET496 (In this case the kinase hinge region) by +-0.4<br />
Edit RSK2-tart/working/rec.crg.pdb to rename "MET A 496" to "MEU A 496"<br />
Edit RSK2-tart/prot.table.ambcrg.ambH to add a MEU amino acid. You can copy the block for MET and rename it to MEU, to polarize the backbone, change the partial charge of the backbone amide proton by +0.4 (i.e. "H MEU 0.648" instead of "H MEU 0.248") lower the backbone carbonyl oxygen by the same quantity ("O MEU -0.500" to "O MEU -0.900")<br />
Edit RSK2-tart/amb.crg.oxt to reflect the same changes<br />
Now all that's left is to run the protein preparation script (blastermaster.py) with the modified parameter files, and without re-protonating the protein:<br />
blastermaster.py --addNOhydrogensflag --chargeFile=/path/to/RSK2-tart/amb.crg.oxt --vdwprottable=/path/to/RSK2-tart/prot.table.ambcrg.ambH<br />
the path for the prot.table.amb.crg.ambH and amb.crg.oxt files should be in the up directory and NOT in the ‘working’ directory.<br />
When the preparation is done, your protein should be "Tarted". You can proceed to docking.<br />
<br />
=== Docking with a co-factor present (waters, orthosteric ligand etc.) ===<br />
Basically it’s the same as tarting.<br />
Add new entry for the co-factor in the prot.table.ambcrg.ambH and amb.crg.oxt files.<br />
Copy these two files to the up directory.<br />
Then run:<br />
blastermaster.py -v --addNOhydrogensflag --chargeFile=/path/to/modified/amb.crg.oxt --vdwprottable=/path/to/modified/prot.table.ambcrg.ambH<br />
<br />
=== Using modified(existing) matching spheres: ===<br />
It is similar to what is done for tarting (see above). Copy the existing spheres into the directory called "/path/working" ("/path" is the directory where you are and contains the rec.pdb and xtal-lig.pdb). It is recommended that this directory, "/path/working", is empty except for the sphere file "match.sph". Then run blastermaster in the directory "/path" as follows: <br />
<br />
blastermaster.py --useExistingMatchingSphflag <br />
<br />
Note that this is a newer feature and is included in DOCK-3.7-beta3 release and later versions.<br />
<br />
=== Using modified(existing) delphi spheres: ===<br />
[[using thin spheres in DOCK3.7]]<br />
<br />
blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag<br />
<br />
=== Changing delphi sphere radii: ===<br />
<br />
blastermaster.py --addNOhydrogensflag --radiusFile=/mnt/nfs/work/dduan/vdw95.siz --chargeFile=/mnt/nfs/work/dduan/001_nociceptin/002_noc_gln_tart/gln670_1_balanced/amb.crg.oxt --vdwprottable=/mnt/nfs/work/dduan/001_nociceptin/002_noc_gln_tart/gln670_1_balanced/prot.table.ambcrg.ambH</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Google_sheets_hit_picking&diff=12249Google sheets hit picking2020-01-28T21:39:27Z<p>Matthew O'Meara: add looking up structures by smiles</p>
<hr />
<div>To display substance 2D structure by smiles<br />
<ol><br />
<li> Put the smiles in column e.g. B2-B100 and then put this formula in the adjacent column</li><br />
<br />
=IMAGE(CONCATENATE("http://zinc15.docking.org/apps/mol/draw.png?smiles=", ENCODEURL(B59)))<br />
<br />
<li> I sometimes have issues with the compounds loading, so it may be useful to save them once they load. Copy column and paste in adjacent column and select "by value" from the drop-down list</li><br />
</ol><br />
<br />
To Displaying substance 2D structure from ZINC_ID<br />
<ol><br />
<li>'''Sort zinc_ids numerically'''. This is really important because otherwise the results won't match up with the right compound.<br />
<ol><br />
<li>Put zinc_ids in a column, e.g. B2-B100'</li><br />
<li>If you try to sort them directly, it will sort them lexigraphically, eg. put ZINC100 before ZINC34. So extract the zinc number from the zinc id by making a column 'ZINC_Number" by putting in cell C2</li><br />
<br />
=VALUE(SUBSTITUTE(B2, "ZINC", ""))<br />
<br />
<li>sort sort the cells by the ZINC_Number column by selecting the whole sheet and then data --> sort range... --> ZINC_Number</li><br />
</li><br />
</ol><br />
<li>To depict the molecules copy and paste the following in each cells in new column. E.g. put this in cell D2 to depict the molecule in B2</li><br />
<br />
=IMAGE(CONCATENATE("http://zinc15.docking.org/substances/", B2, "-small.png"))<br />
<br />
<li>Use IMPORTDATA to populate additional columns of interest in the header of the next columns. It looks like it can only load 3 columns at a time, so for example put the first cell D1, the next . Look up additional columns of interest here http://zinc15.docking.org/substances/help/. As a sanity check include the zinc_id in the output column and verify that it corresponds with the input column</li><br />
<br />
Put in cell E1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=zinc_id smiles mol_formula logp"))<br />
Put in cell I1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=mwt num_chiral_centers reactivity"))<br />
Put in cell L1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=predicted_gene_names purchasability supplier_codes"))<br />
</ol></div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=AMSOL&diff=11867AMSOL2019-07-15T20:05:08Z<p>Matthew O'Meara: add description of how to allow amsol to work with large molecules</p>
<hr />
<div>From the [http://comp.chem.umn.edu/amsol/ AMSOL Web Site]:<br />
<br />
AMSOL is a semiempirical quantum chemistry program that includes the MINDO/3, MNDO, AM1, and PM3 gas-phase Hamiltonians, the CM1A, CM1P, CM2/AM1, CM2/PM3, CM3/AM1, and CM3/PM3 charge models for calculating partial atomic charges, the SM1 - SM5.42R solvation models for calculating free energies of solvation in water, the SM4 solvation model for calculating free energies of solvation in alkanes, and the SM5.42R, SM5.4, SM5.2R, and SM5.0R solvation models for calculating free energies of solvation in any organic solvent. Most of the solvation models are based on the AM1 and/or PM3 Hamiltonians; the SM5.2R model is also available with the MNDO Hamiltonian. AMSOL can also accept user-specified specific reaction parameters. All solvation models that are denoted with an "R" in their name are for rigid-solute calculations and were designed to utilize accurate gas-phase geometries to predict solvation free energies. For all other models, geometry optimization is possible in both the gas phase and solution. For SM5.4 models analytic derivatives are available for geometry optimization.<br />
<br />
* AMSOL is used by [[ZINC]].<br />
<br />
==Installation==<br />
Go here: https://secure.nouvant.com/umn/technology/z05201/license/153/agreements/new<br />
Install this on sgehead: ~]# <br />
yum install compat-gcc-34-g77.x86_64<br />
Fill in the license information. <br /><br />
Download the gzip file.<br /><br />
Unzip it.<br /><br />
Change into the directory and run the amsol.compile file.<br /><br />
<br />
== Compiling ==<br />
If you're on a newer Linux machine and get errors compiling, then you may need to apply the following changes to '''new/amsol.f''':<br />
<pre><br />
26,27c26,27<br />
< OPEN(19,NAME='fort.19') BJL1003<br />
< OPEN(20,NAME='fort.20') BJL1003<br />
---<br />
> OPEN(19,file='fort.19') BJL1003<br />
> OPEN(20,file='fort.20') BJL1003<br />
</pre><br />
<br />
If you don't know what that means, then just find the file '''new/amsol.f''' and find lines 26 and 27 which should be<br />
OPEN(19,NAME='fort.19') BJL1003<br />
OPEN(20,NAME='fort.20') BJL1003<br />
and replace that with<br />
OPEN(19,file='fort.19') BJL1003<br />
OPEN(20,file='fort.20') BJL1003<br />
<br />
===Patches===<br />
For using Amsol7.1 with dock3.7, we distribute a patch: <br />
$DOCKBASE/ligand/amsol/patches/amsol7.1_port_intcar.f.diff<br />
<br />
This patch resolve an issue with linear molecules. <br />
<br />
Consider applying this patch and then recompile amsol7.1.<br />
<br />
===Large Molecules===<br />
By default AMSOL limits the number of heavy atoms to 60 and the number of light atoms (i.e. hydrogens) to 60. To increase the limit,<br />
in '''include/SIZES.i''' edit the following line<br />
<br />
PARAMETER (MAXHEV=60, MAXLIT=60, NCHAIN=60, NRELAX=25) DL0397<br />
<br />
to, for example,<br />
<br />
PARAMETER (MAXHEV=80, MAXLIT=110, NCHAIN=60, NRELAX=25) DL0397<br />
<br />
and recompile by running make in the base directory<br />
<br />
make<br />
<br />
<br />
<br />
<br />
[[Category:Solvation]]<br />
[[Category:Software]]<br />
[[Category:Freecom]]</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Google_sheets_hit_picking&diff=11772Google sheets hit picking2019-06-13T16:57:58Z<p>Matthew O'Meara: </p>
<hr />
<div>To use Google sheets for hit-picking<br />
<br />
<ol><br />
<li>'''Sort zinc_ids numerically'''. This is really important because otherwise the results won't match up with the right compound.<br />
<ol><br />
<li>Put zinc_ids in a column, e.g. B2-B100'</li><br />
<li>If you try to sort them directly, it will sort them lexigraphically, eg. put ZINC100 before ZINC34. So extract the zinc number from the zinc id by making a column 'ZINC_Number" by putting in cell C2</li><br />
<br />
=VALUE(SUBSTITUTE(B2, "ZINC", ""))<br />
<br />
<li>sort sort the cells by the ZINC_Number column by selecting the whole sheet and then data --> sort range... --> ZINC_Number</li><br />
</li><br />
</ol><br />
<li>To depict the molecules copy and paste the following in each cells in new column. E.g. put this in cell D2 to depict the molecule in B2</li><br />
<br />
=IMAGE(CONCATENATE("http://zinc15.docking.org/substances/", B2, "-small.png"))<br />
<br />
<li>Use IMPORTDATA to populate additional columns of interest in the header of the next columns. It looks like it can only load 3 columns at a time, so for example put the first cell D1, the next . Look up additional columns of interest here http://zinc15.docking.org/substances/help/. As a sanity check include the zinc_id in the output column and verify that it corresponds with the input column</li><br />
<br />
Put in cell E1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=zinc_id smiles mol_formula logp"))<br />
Put in cell I1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=mwt num_chiral_centers reactivity"))<br />
Put in cell L1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=predicted_gene_names purchasability supplier_codes"))<br />
</ol></div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=JupyterNotebook&diff=11602JupyterNotebook2019-03-28T19:12:49Z<p>Matthew O'Meara: Basics for setting up Jupyter Notebook</p>
<hr />
<div><br />
= Using Jupyter Notebooks =<br />
<br />
== jupyter ports ==<br />
Talk to Ben about getting a port range set up for you<br />
{| class="wikitable"<br />
|-<br />
! Lab Member<br />
! Port range<br />
|-<br />
| Matthew O'Meara<br />
| 5040-5049<br />
|-<br />
|}<br />
<br />
<br />
== install dependencies ==<br />
Install conda environment for python, typically I use<br />
<br />
<br />
conda create -n main anaconda<br />
source activate main<br />
<br />
Start the notebook server<br />
<br />
# set the jupyter port (see above)<br />
JUPYTER_PORT=5048<br />
<br />
# on gimel in the bkslab cluster<br />
jupyter notebook --ip=0.0.0.0 --port=$JUPYTER_PORT<br />
# copy the token e.g. 'e0593317037148392cb9b0489a5f376ca950f3a14d37e371' to the clipboard<br />
<br />
log in to the notebook server from a client<br />
<br />
# on a laptop outside the lab network<br />
JUPYTER_PORT=5048<br />
ssh -N -p 22 -D 1080 momeara@portal.ucsf.bkslab.org -L $JUPYTER_PORT:gimel:$JUPYTER_PORT<br />
# open a web browser and navigate to localhost:JUPYTER_PORT/lab and enter the token<br />
<br />
== Tips ==<br />
* use localhost:JUPYTER_PORT/'''lab''' to get the JuypterLab interface, its much better but for some reason not the default yet</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Google_sheets_hit_picking&diff=11519Google sheets hit picking2019-02-27T17:44:32Z<p>Matthew O'Meara: </p>
<hr />
<div>To use Google sheets for hit-picking<br />
<br />
<ol><br />
<li>'''Sort zinc_ids numerically'''. This is really important because otherwise the results won't match up with the right compound.<br />
<ol><br />
<li>Put zinc_ids in a column, e.g. B2-B100'</li><br />
<li>If you try to sort them directly, it will sort them lexigraphically, eg. put ZINC100 before ZINC34. So extract the zinc number from the zinc id by making a column 'ZINC_Number" by putting in cell C2</li><br />
<br />
=VALUE(SUBSTITUTE(B2, "ZINC", ""))<br />
<br />
<li>sort sort the cells by the ZINC_Number column by selecting the whole sheet and then data --> sort range... --> ZINC_Number</li><br />
</li><br />
</ol><br />
<li>To depict the molecules copy and paste the following in each cells in new column. E.g. put this in cell D2 to depict the molecule in B2</li><br />
<br />
=IMAGE(CONCATENATE("http://zinc15.docking.org/substances/", B2, "-small.png"))<br />
<br />
<li>Use IMPORTDATA to populate additional columns of interest in the header of the next columns. It looks like it can only load 3 columns at a time, so for example put the first cell D1, the next . Look up additional columns of interest here `http://zinc15.docking.org/substances/help/`. As a sanity check include the zinc_id in the output column and verify that it corresponds with the input column</li><br />
<br />
Put in cell E1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=zinc_id smiles mol_formula logp"))<br />
Put in cell I1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=mwt num_chiral_centers reactivity"))<br />
Put in cell L1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=predicted_gene_names purchasability supplier_codes"))<br />
</ol></div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Google_sheets_hit_picking&diff=11518Google sheets hit picking2019-02-27T17:38:59Z<p>Matthew O'Meara: </p>
<hr />
<div>To use Google sheets for hit-picking<br />
<br />
1. '''Sort zinc_ids numerically'''. This is really important because otherwise the results won't match up with the right compound.<br />
a. Put zinc_ids in a column, e.g. B2-B100'<br />
b. If you try to sort them directly, it will sort them lexigraphically, eg. put ZINC100 before ZINC34. So extract the zinc number from the zinc id by making a column 'ZINC_Number" by putting in cell C2<br />
<br />
=VALUE(SUBSTITUTE(B2, "ZINC", ""))<br />
<br />
c. sort sort the cells by the ZINC_Number column by selecting the whole sheet and then data --> sort range... --> ZINC_Number<br />
<br />
2. To depict the molecules copy and paste the following in each cells in new column. E.g. put this in cell D2 to depict the molecule in B2<br />
<br />
=IMAGE(CONCATENATE("http://zinc15.docking.org/substances/", B2, "-small.png"))<br />
<br />
3. Use IMPORTDATA to populate additional columns of interest in the header of the next columns. It looks like it can only load 3 columns at a time, so for example put the first cell D1, the next . Look up additional columns of interest here `http://zinc15.docking.org/substances/help/`. As a sanity check include the zinc_id in the output column and verify that it corresponds with the input column<br />
<br />
Put in cell E1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=zinc_id smiles mol_formula logp"))<br />
Put in cell I1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=mwt num_chiral_centers reactivity"))<br />
Put in cell L1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=predicted_gene_names purchasability supplier_codes"))</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Google_sheets_hit_picking&diff=11517Google sheets hit picking2019-02-27T17:38:29Z<p>Matthew O'Meara: more details on how to sort by zinc number</p>
<hr />
<div>To use Google sheets for hit-picking<br />
<br />
1. '''Sort zinc_ids numerically'''. This is really important because otherwise the results won't match up with the right compound.<br />
a. Put zinc_ids in a column, e.g. B2-B100'<br />
b. If you try to sort them directly, it will sort them lexigraphically, eg. put ZINC100 before ZINC34. So extract the zinc number from the zinc id by making a column 'ZINC_Number" by putting in cell C2<br />
<br />
=VALUE(SUBSTITUTE(B2, 'ZINC', ''))<br />
<br />
c. sort sort the cells by the ZINC_Number column by selecting the whole sheet and then data --> sort range... --> ZINC_Number<br />
<br />
2. To depict the molecules copy and paste the following in each cells in new column. E.g. put this in cell D2 to depict the molecule in B2<br />
<br />
=IMAGE(CONCATENATE("http://zinc15.docking.org/substances/", B2, "-small.png"))<br />
<br />
3. Use IMPORTDATA to populate additional columns of interest in the header of the next columns. It looks like it can only load 3 columns at a time, so for example put the first cell D1, the next . Look up additional columns of interest here `http://zinc15.docking.org/substances/help/`. As a sanity check include the zinc_id in the output column and verify that it corresponds with the input column<br />
<br />
Put in cell E1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=zinc_id smiles mol_formula logp"))<br />
Put in cell I1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=mwt num_chiral_centers reactivity"))<br />
Put in cell L1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=predicted_gene_names purchasability supplier_codes"))</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Google_sheets_hit_picking&diff=11516Google sheets hit picking2019-02-27T17:01:14Z<p>Matthew O'Meara: </p>
<hr />
<div>To use Google sheets for hit-picking<br />
<br />
1. '''Put zinc_ids in sorted order in a column, e.g. B2-B100'''<br />
<br />
2. To depict the molecules copy and paste the following in each cells in new column. E.g. put this in cell C2 to depict the molecule in B2<br />
<br />
=IMAGE(CONCATENATE("http://zinc15.docking.org/substances/", B2, "-small.png"))<br />
<br />
3. Use IMPORTDATA to populate additional columns of interest in the header of the next columns. It looks like it can only load 3 columns at a time, so for example put the first cell D1, the next . Look up additional columns of interest here `http://zinc15.docking.org/substances/help/`<br />
<br />
Put in cell D1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=smiles mol_formula logp"))<br />
Put in cell G1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=mwt num_chiral_centers reactivity"))<br />
Put in cell K1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=predicted_gene_names purchasability supplier_codes"))</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Sea16_restart&diff=11450Sea16 restart2019-01-14T18:10:09Z<p>Matthew O'Meara: </p>
<hr />
<div><pre><br />
<br />
<br />
# restart conda_sea16 server<br />
<br />
screen -r sea16 on gimel<br />
cd /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/src/seaware-academic/<br />
export PATH=/nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/bin:$PATH<br />
export PATH=/nfs/home/momeara/opt/bin:$PATH<br />
# In particular this needs the path to 'svgo' to optimize images of compounds to be sent to client<br />
<br />
source activate sea16 <br />
sh SEAserver/scripts/stop-sea-server.sh production<br />
sh SEAserver/scripts/run-sea-server.sh production<br />
<br />
<br />
# update conda_sea16<br />
<br />
ssh s_enkhee@gimel<br />
su - www<br />
cd /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/src/seaware-academic/<br />
export PATH=/nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/bin:$PATH<br />
export PATH=/nfs/home/momeara/opt/bin:$PATH<br />
source activate sea16<br />
git pull<br />
git submodule update --init --recursive<br />
kill all sea-server related processes e.g. from htop<br />
make clean<br />
delete sea related libraries (fitcore, fpcore, libcore, seacore, seashell, seaserver) from your site-packages folder under the conda env<br />
rm -rf /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/lib/python2.7/site-packages/seaserver <br />
make all<br />
make SEAserver-start-production <br />
<br />
# run the test:<br />
-> export SEA_APP_ROOT=$CONDA_PREFIX/var/seaserver<br />
-> export SEA_RUN_FOLDER=$SEA_APP_ROOT/run<br />
-> export SEA_DATA_FOLDER=$SEA_APP_ROOT/data<br />
-> python -m unittest test.test_illustrate<br />
<br />
<br />
# Redis config<br />
<br />
As for the Redis warnings, these are not new, but probably something worth taking care of (https://redis.io/topics/admin):<br />
<br />
add 'vm.overcommit_memory = 1' to /etc/sysctl.conf<br />
<br />
From here: The Linux kernel will always overcommit memory, and never check if enough memory is available. This increases the risk of out-of-memory situations, but also improves memory-intensive workloads.<br />
<br />
run echo never > /sys/kernel/mm/transparent_hugepage/enabled<br />
add 'echo never > /sys/kernel/mm/transparent_hugepage/enabled' to /etc/rc.local<br />
<br />
From here: Latency induced by transparent huge pages<br />
<br />
Unfortunately when a Linux kernel has transparent huge pages enabled, Redis incurs to a big latency penalty after the fork call is used in order to persist on disk. Huge pages are the cause of the following issue:<br />
<br />
Fork is called, two processes with shared huge pages are created.<br />
In a busy instance, a few event loops runs will cause commands to target a few thousand of pages, causing the copy on write of almost the whole process memory.<br />
This will result in big latency and big memory usage.<br />
<br />
Make sure to disable transparent huge pages using the following command:<br />
<br />
echo never > /sys/kernel/mm/transparent_hugepage/enabled<br />
<br />
<br />
<br />
<br />
<br />
# update sea16<br />
ssh xyz@gimel<br />
cd /nfs/soft/www/apps/sea/sea16/src/seaware-academic<br />
source ../../env.csh<br />
git pull<br />
rm -rf /nfs/soft/www/apps/sea/sea16/lib/python2.7/site-packages/seaserver<br />
cd /nfs/soft/www/apps/sea/sea16/src/seaware-academic/SEAserver<br />
python setup.py install<br />
<br />
# restart server<br />
<br />
ssh www@n-1-110<br />
cd /nfs/soft/www/apps/sea/sea16/src/seaware-academic<br />
source ../../env.csh<br />
cd SEAsever<br />
sh scripts/run-sea-server.sh<br />
<br />
# restart server<br />
<br />
ssh <superuser>@n-1-110<br />
sudo -i<br />
screen -r<br />
screen -dR Sea (switch to sea screen)<br />
sh scripts/run-sea-server.sh<br />
<br />
# how to save the old queue data<br />
<br />
cd /nfs/soft/www/apps/sea/sea16/var/seaserver/queue <br />
mv jobs jobs.save<br />
mv tasks.sqlite tasks.sqllite.save <br />
restart sea server on n-1-110. <br />
<br />
(basically, it had too much history and that was what was slowing it down)<br />
(do on the first day of the month and rename the old one to a month version)<br />
<br />
<br />
</pre><br />
<br />
[[Category:Curator]]</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Google_sheets_hit_picking&diff=11103Google sheets hit picking2018-12-17T17:49:16Z<p>Matthew O'Meara: how to use google sheets for hit-picking</p>
<hr />
<div>To use Google sheets for hit-picking<br />
<br />
1. Put zinc_ids in sorted order in a column, e.g. B2-B100<br />
2. To depict the molecules copy and paste the following in each cells in new column. E.g. put this in cell C2 to depict the molecule in B2<br />
<br />
=IMAGE(CONCATENATE("http://zinc15.docking.org/substances/", B2, "-small.png"))<br />
<br />
3. Use IMPORTDATA to populate additional columns of interest in the header of the next columns. It looks like it can only load 3 columns at a time, so for example put the first cell D1, the next . Look up additional columns of interest here `http://zinc15.docking.org/substances/help/`<br />
<br />
Put in cell D1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=smiles mol_formula logp"))<br />
Put in cell G1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=mwt num_chiral_centers reactivity"))<br />
Put in cell K1: =IMPORTDATA(CONCATENATE("http://zinc15.docking.org/substances.csv?zinc_id-in=", JOIN("+", B2:B100),"&output_fields=predicted_gene_names supplier_codes"))</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Category:PyTorch&diff=11096Category:PyTorch2018-12-11T06:12:45Z<p>Matthew O'Meara: PyTorch</p>
<hr />
<div>I (Matt O'Meara) got pytorch installed December 2018<br />
<br />
bash<br />
<br />
#(DeepSEA_local) bash-4.1$ uname -a<br />
#Linux gimel2.cluster.ucsf.bkslab.org 2.6.32-754.6.3.el6.x86_64 #1 SMP Tue Oct 9 17:27:49 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux<br />
<br />
#(DeepSEA_local) bash-4.1$ gcc -v<br />
#Using built-in specs.<br />
#COLLECT_GCC=gcc<br />
#COLLECT_LTO_WRAPPER=/mnt/nfs/home/momeara/opt/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper<br />
#Target: x86_64-unknown-linux-gnu<br />
#Configured with: ./configure --prefix=/mnt/nfs/home/momeara/opt/<br />
#Thread model: posix<br />
#gcc version 4.9.3 (GCC)<br />
<br />
export CC="/mnt/nfs/home/momeara/opt/bin/gcc"<br />
export CXX="/mnt/nfs/home/momeara/opt/bin/g++"<br />
export CPLUS_INCLUDE_PATH="/mnt/nfs/home/momeara/opt/include:/nfs/soft/cuda/include"<br />
export C_INCLUDE_PATH="/mnt/nfs/home/momeara/opt/include:/nfs/soft/cuda/include"<br />
export LIBRARY_PATH="/mnt/nfs/home/momeara/opt/lib:/mnt/nfs/home/momeara/opt/lib64:/nfs/soft/cuda/lib64"<br />
export LD_LIBRARY_PATH="/nfs/home/momeara/ex9/collaborations/DeepSEA/cuda/lib64:$LD_LIBRARY_PATH"<br />
export LD_LIBRARY_PATH="/nfs/soft/cuda/lib64:$LD_LIBRARY_PATH"<br />
export LD_LIBRARY_PATH="/nfs/soft/cuda10.0/extras/CUPTI/lib64:$LD_LIBRARY_PATH"<br />
export LD_LIBRARY_PATH="/mnt/nfs/home/momeara/opt/lib:/mnt/nfs/home/momeara/opt/lib64:$LD_LIBRARY_PATH"<br />
export LD_LIBRARY_PATH="/nfs/home/momeara/ex9/collaborations/DeepSEA/nccl/nccl_2.3.5-2+cuda9.0_x86_64/lib:/nfs/soft/cuda-10.0/lib64:$LD_LIBRARY_PATH"<br />
export PATH="/nfs/soft/cuda10.0/bin:$PATH"<br />
export PATH="/nfs/ex9/work/momeara/tools/anaconda3//bin:$PATH"<br />
export PATH="/nfs/ex9/work/momeara/tools/anaconda3/envs/DeepSEA_local/bin:$PATH"<br />
<br />
cd ~/ex9/collaborations/DeepSEA/pytorch<br />
git clone --recursive https://github.com/pytorch/pytorch<br />
cd pytorch<br />
git fetch --all --tags --prune<br />
git checkout db5d3131d16f57abd4f13d3f4b885d5f67bf6644 #v1.0.0 branch</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Tunnel_how_to&diff=11024Tunnel how to2018-10-04T17:33:55Z<p>Matthew O'Meara: </p>
<hr />
<div>ssh -D 8090 sgehead.uoft.bkslab.org<br />
chrome->settings->network->proxy->socks proxy<br />
host: localhost<br />
port: 8090<br />
<br />
== new way ==<br />
open shell on laptop<br />
ssh -vNL localhost:2222:gimel:22 -D1080 portalxxx.ucsf.bkslab.org <br />
<br />
Then use switchyomega in chrome to use socks5 to localhost 1080<br />
<br />
For ssh use<br />
scp -P 2222 localhost:cshrc.save . <br />
<br />
<br />
==Rsync through tunnel==<br />
<br />
To send a file /tmp/my_temp_file on your laptop to gimel, first setup a tunnel<br />
<br />
ssh -N -p 22 -D 1080 <username>@portal.ucsf.bkslab.org -L 2222:gimel:22<br />
<br />
then in a new terminal<br />
<br />
rsync -Phavz -e "ssh -p 2222" /tmp/my_temp_file localhost:/tmp/<br />
<br />
<br />
[Category:jji]]<br />
<br />
Tunelling<br />
ssh private network<br />
<br />
<br />
[[File:Switchyomega autoswitch.png]]<br />
[[File:SwitchyOmega 1080tunnel.png]]</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=10579Contract Research Organizations2018-03-26T21:04:11Z<p>Matthew O'Meara: /* Other CROs */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They are routinely used by Henry Lin, Matthew O'Meara, and Josh Pottel (2013-2017) and they gave reasonable results at reasonable prices. Note the bulk order discount is for all of UCSF, so no need to try to make large orders.<br />
<br />
The shoichet lab contact there has been (01/17):<br />
John Vu, phone #: 510 227 9213, email: JohnVu@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
In particular they have a protease panel covering over 70 proteases and can possibly develop further targets<br />
<br />
==[http://www.alfa-chemistry.com Alfa Chemistry]==<br />
They offer an extensive catalog of building blocks, reagents, catalysts, reference materials, and research chemicals in a wide range of applications. We also provide analytical services and laboratory services to our customers.<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
3,500 minimum order size e.g. 1 compound at 5 receptors at 10 doses each<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==[http://www.cyprotex.com/toxicology Cyprotex]==<br />
Cyprotex is a contract research organization specializing in preclinical ADME-Tox with offices in the UK and US.<br />
<br />
Permeability & Transporters<br />
* Caco-2 permeability<br />
* Transporter interactions<br />
* PAMPA-GI and PAMPA-BBB<br />
* MDCK and MDR1-MDCK<br />
* Transdermal absorption<br />
* Intranasal absorption<br />
<br />
Distribution - reversible/time dependent<br />
* Plasma protein binding<br />
* Whole blood binding<br />
* Blood to plasma ratio<br />
* Brain tissue binding<br />
* Microsomal binding<br />
<br />
Metabolism<br />
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood<br />
* Metabolite profiling and identification<br />
* Reaction phenotyping<br />
* CYP inhibition<br />
* UGT inhibition<br />
* MAO inhibition<br />
* CYP induction<br />
* PXR and AhR nuclear <br />
<br />
receptor activation<br />
* 3D microtissues<br />
<br />
==[http://www.brunswicklabs.com/biological-analysis Brunswick Labs]==<br />
Brunswick Laboratories is an independent, full-service bioanalytical laboratory specializing in the science of Antioxidants, Oxidative Stress, Anti-inflammatory, Synthetic and Natural Compound Bioanalysis.<br />
<br />
+1-508-281-6660<br />
blservices@brunswicklabs.com<br />
200 Turnpike Road, Southborough, MA 01772, USA<br />
<br />
* Bioavailability, BioAbsorption, and BioUptake study via Caco-2 human intestinal cells<br />
* Anti-inflammatory: LOX, COX, TNF-alpha, NFkB, Interleukins (ILs), and PGE2 as biomarkers<br />
* Oxidative Stress Analysis for biological samples<br />
* Antioxidation effect in a biological system: Nrf2, Cellular Antioxidant Assay (CAA) <br />
* Diabetes and Weight Management: insulin secretion, insulin receptor activity, glucose uptake, glucose metabolism, and carbohydrate digestion as biomarkers<br />
* Detoxification and Liver Function: Phase I and Phase II liver enzymes, liver function biomakers in serum<br />
* Energy metabolism investigation via human cells <br />
* Anti-cancer Function evaluation: cancer cell viability, proliferation, apoptosis, and invasion as biomarkers <br />
* Anti-aging Assays: SIRT-1, telomerase activity as biomarkers<br />
* Preclinical Investigations for Skin Care Products: UV protection, melanin (age spot) inhibition, anti-aging, anti-inflammatory<br />
<br />
==[http://biotoxsciences.com/In_Vitro_Services BioToxSciences]==<br />
http://biotoxsciences.com/In_Vitro_Services<br />
<br />
Based in San Diego, they have a range of in-vitro functional assays<br />
<br />
==Other CROs==<br />
* [http://www.alfa-chemistry.com Alfa Chemistry]<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.bocsci.com BOC Sciences]Drug Discovery <br />
* [http://www.creative-peptides.com Creative Peptides]peptide<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs<br />
* [http://www.creative-biogene.com/ Creative Biogene] Transfected Stable Cell Lines<br />
* [http://www.creative-bioarray.com/ Creative Bioarray] Human Umbilical Cord Primary Cells<br />
* [https://www.confluencediscovery.com/ Confluence Discovery Technologies]<br />
** Contact: Jeff Hirsch <jhirsch@confluencestl.com><br />
** Biomarker, Immuno-Oncology, Enzymology<br />
*<br />
<br />
== CRO sourcing services ==<br />
* [https://www.scienceexchange.com]<br />
* [https://www.assaydepot.com]<br />
<br />
https://www.genoway.com/services/catalog-models/mouse-knockouts.htm?utm_source=emailing&utm_medium=email&utm_content=01122015&utm_campaign=01122015</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=10578Contract Research Organizations2018-03-26T21:03:57Z<p>Matthew O'Meara: /* Other CROs */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They are routinely used by Henry Lin, Matthew O'Meara, and Josh Pottel (2013-2017) and they gave reasonable results at reasonable prices. Note the bulk order discount is for all of UCSF, so no need to try to make large orders.<br />
<br />
The shoichet lab contact there has been (01/17):<br />
John Vu, phone #: 510 227 9213, email: JohnVu@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
In particular they have a protease panel covering over 70 proteases and can possibly develop further targets<br />
<br />
==[http://www.alfa-chemistry.com Alfa Chemistry]==<br />
They offer an extensive catalog of building blocks, reagents, catalysts, reference materials, and research chemicals in a wide range of applications. We also provide analytical services and laboratory services to our customers.<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
3,500 minimum order size e.g. 1 compound at 5 receptors at 10 doses each<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==[http://www.cyprotex.com/toxicology Cyprotex]==<br />
Cyprotex is a contract research organization specializing in preclinical ADME-Tox with offices in the UK and US.<br />
<br />
Permeability & Transporters<br />
* Caco-2 permeability<br />
* Transporter interactions<br />
* PAMPA-GI and PAMPA-BBB<br />
* MDCK and MDR1-MDCK<br />
* Transdermal absorption<br />
* Intranasal absorption<br />
<br />
Distribution - reversible/time dependent<br />
* Plasma protein binding<br />
* Whole blood binding<br />
* Blood to plasma ratio<br />
* Brain tissue binding<br />
* Microsomal binding<br />
<br />
Metabolism<br />
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood<br />
* Metabolite profiling and identification<br />
* Reaction phenotyping<br />
* CYP inhibition<br />
* UGT inhibition<br />
* MAO inhibition<br />
* CYP induction<br />
* PXR and AhR nuclear <br />
<br />
receptor activation<br />
* 3D microtissues<br />
<br />
==[http://www.brunswicklabs.com/biological-analysis Brunswick Labs]==<br />
Brunswick Laboratories is an independent, full-service bioanalytical laboratory specializing in the science of Antioxidants, Oxidative Stress, Anti-inflammatory, Synthetic and Natural Compound Bioanalysis.<br />
<br />
+1-508-281-6660<br />
blservices@brunswicklabs.com<br />
200 Turnpike Road, Southborough, MA 01772, USA<br />
<br />
* Bioavailability, BioAbsorption, and BioUptake study via Caco-2 human intestinal cells<br />
* Anti-inflammatory: LOX, COX, TNF-alpha, NFkB, Interleukins (ILs), and PGE2 as biomarkers<br />
* Oxidative Stress Analysis for biological samples<br />
* Antioxidation effect in a biological system: Nrf2, Cellular Antioxidant Assay (CAA) <br />
* Diabetes and Weight Management: insulin secretion, insulin receptor activity, glucose uptake, glucose metabolism, and carbohydrate digestion as biomarkers<br />
* Detoxification and Liver Function: Phase I and Phase II liver enzymes, liver function biomakers in serum<br />
* Energy metabolism investigation via human cells <br />
* Anti-cancer Function evaluation: cancer cell viability, proliferation, apoptosis, and invasion as biomarkers <br />
* Anti-aging Assays: SIRT-1, telomerase activity as biomarkers<br />
* Preclinical Investigations for Skin Care Products: UV protection, melanin (age spot) inhibition, anti-aging, anti-inflammatory<br />
<br />
==[http://biotoxsciences.com/In_Vitro_Services BioToxSciences]==<br />
http://biotoxsciences.com/In_Vitro_Services<br />
<br />
Based in San Diego, they have a range of in-vitro functional assays<br />
<br />
==Other CROs==<br />
* [http://www.alfa-chemistry.com Alfa Chemistry]<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.bocsci.com BOC Sciences]Drug Discovery <br />
* [http://www.creative-peptides.com Creative Peptides]peptide<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs<br />
* [http://www.creative-biogene.com/ Creative Biogene] Transfected Stable Cell Lines<br />
* [http://www.creative-bioarray.com/ Creative Bioarray] Human Umbilical Cord Primary Cells<br />
* [https://www.confluencediscovery.com/ Confluence Discovery Technologies<br />
** Contact: Jeff Hirsch <jhirsch@confluencestl.com><br />
** Biomarker, Immuno-Oncology, Enzymology<br />
*<br />
<br />
== CRO sourcing services ==<br />
* [https://www.scienceexchange.com]<br />
* [https://www.assaydepot.com]<br />
<br />
https://www.genoway.com/services/catalog-models/mouse-knockouts.htm?utm_source=emailing&utm_medium=email&utm_content=01122015&utm_campaign=01122015</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Sea16_restart&diff=10277Sea16 restart2017-09-05T14:08:16Z<p>Matthew O'Meara: </p>
<hr />
<div><pre><br />
<br />
<br />
# restart conda_sea16 server<br />
<br />
screen -r sea16 on gimel<br />
cd /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/src/seaware-academic/<br />
export PATH=/nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/bin:$PATH<br />
export PATH=/nfs/home/momeara/opt/bin:$PATH<br />
source activate sea16 <br />
sh SEAserver/scripts/stop-sea-server.sh production<br />
sh SEAserver/scripts/run-sea-server.sh production<br />
<br />
<br />
# update conda_sea16<br />
<br />
ssh s_enkhee@gimel<br />
su - www<br />
cd /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/src/seaware-academic/<br />
export PATH=/nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/bin:$PATH<br />
export PATH=/nfs/home/momeara/opt/bin:$PATH<br />
source activate sea16<br />
git pull<br />
git submodule update --init --recursive<br />
kill all sea-server related processes e.g. from htop<br />
make clean<br />
delete sea related libraries (fitcore, fpcore, libcore, seacore, seashell, seaserver) from your site-packages folder under the conda env<br />
rm -rf /nfs/soft/www/apps/sea/conda_sea16/anaconda2/envs/sea16/lib/python2.7/site-packages/seaserver <br />
make all<br />
make SEAserver-start-production <br />
<br />
# run the test:<br />
-> export SEA_APP_ROOT=$CONDA_PREFIX/var/seaserver<br />
-> export SEA_RUN_FOLDER=$SEA_APP_ROOT/run<br />
-> export SEA_DATA_FOLDER=$SEA_APP_ROOT/data<br />
-> python -m unittest test.test_illustrate<br />
<br />
<br />
# Redis config<br />
<br />
As for the Redis warnings, these are not new, but probably something worth taking care of (https://redis.io/topics/admin):<br />
<br />
add 'vm.overcommit_memory = 1' to /etc/sysctl.conf<br />
<br />
From here: The Linux kernel will always overcommit memory, and never check if enough memory is available. This increases the risk of out-of-memory situations, but also improves memory-intensive workloads.<br />
<br />
run echo never > /sys/kernel/mm/transparent_hugepage/enabled<br />
add 'echo never > /sys/kernel/mm/transparent_hugepage/enabled' to /etc/rc.local<br />
<br />
From here: Latency induced by transparent huge pages<br />
<br />
Unfortunately when a Linux kernel has transparent huge pages enabled, Redis incurs to a big latency penalty after the fork call is used in order to persist on disk. Huge pages are the cause of the following issue:<br />
<br />
Fork is called, two processes with shared huge pages are created.<br />
In a busy instance, a few event loops runs will cause commands to target a few thousand of pages, causing the copy on write of almost the whole process memory.<br />
This will result in big latency and big memory usage.<br />
<br />
Make sure to disable transparent huge pages using the following command:<br />
<br />
echo never > /sys/kernel/mm/transparent_hugepage/enabled<br />
<br />
<br />
<br />
<br />
<br />
# update sea16<br />
ssh xyz@gimel<br />
cd /nfs/soft/www/apps/sea/sea16/src/seaware-academic<br />
source ../../env.csh<br />
git pull<br />
rm -rf /nfs/soft/www/apps/sea/sea16/lib/python2.7/site-packages/seaserver<br />
cd /nfs/soft/www/apps/sea/sea16/src/seaware-academic/SEAserver<br />
python setup.py install<br />
<br />
# restart server<br />
<br />
ssh www@n-1-110<br />
cd /nfs/soft/www/apps/sea/sea16/src/seaware-academic<br />
source ../../env.csh<br />
cd SEAsever<br />
sh scripts/run-sea-server.sh<br />
<br />
# restart server<br />
<br />
ssh <superuser>@n-1-110<br />
sudo -i<br />
screen -r<br />
screen -dR Sea (switch to sea screen)<br />
sh scripts/run-sea-server.sh<br />
<br />
# how to save the old queue data<br />
<br />
cd /nfs/soft/www/apps/sea/sea16/var/seaserver/queue <br />
mv jobs jobs.save<br />
mv tasks.sqlite tasks.sqllite.save <br />
restart sea server on n-1-110. <br />
<br />
(basically, it had too much history and that was what was slowing it down)<br />
(do on the first day of the month and rename the old one to a month version)<br />
<br />
<br />
</pre><br />
<br />
[[Category:Curator]]</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=9977Contract Research Organizations2017-03-23T18:10:34Z<p>Matthew O'Meara: /* GenScript */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They are routinely used by Henry Lin, Matthew O'Meara, and Josh Pottel (2013-2017) and they gave reasonable results at reasonable prices. Note the bulk order discount is for all of UCSF, so no need to try to make large orders.<br />
<br />
The shoichet lab contact there has been (01/17):<br />
John Vu, phone #: 510 227 9213, email: JohnVu@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
In particular they have a protease panel covering over 70 proteases and can possibly develop further targets<br />
<br />
==[http://www.alfa-chemistry.com Alfa Chemistry]==<br />
They offer an extensive catalog of building blocks, reagents, catalysts, reference materials, and research chemicals in a wide range of applications. We also provide analytical services and laboratory services to our customers.<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
3,500 minimum order size e.g. 1 compound at 5 receptors at 10 doses each<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==[http://www.cyprotex.com/toxicology Cyprotex]==<br />
Cyprotex is a contract research organization specializing in preclinical ADME-Tox with offices in the UK and US.<br />
<br />
Permeability & Transporters<br />
* Caco-2 permeability<br />
* Transporter interactions<br />
* PAMPA-GI and PAMPA-BBB<br />
* MDCK and MDR1-MDCK<br />
* Transdermal absorption<br />
* Intranasal absorption<br />
<br />
Distribution - reversible/time dependent<br />
* Plasma protein binding<br />
* Whole blood binding<br />
* Blood to plasma ratio<br />
* Brain tissue binding<br />
* Microsomal binding<br />
<br />
Metabolism<br />
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood<br />
* Metabolite profiling and identification<br />
* Reaction phenotyping<br />
* CYP inhibition<br />
* UGT inhibition<br />
* MAO inhibition<br />
* CYP induction<br />
* PXR and AhR nuclear <br />
<br />
receptor activation<br />
* 3D microtissues<br />
<br />
==[http://www.brunswicklabs.com/biological-analysis Brunswick Labs]==<br />
Brunswick Laboratories is an independent, full-service bioanalytical laboratory specializing in the science of Antioxidants, Oxidative Stress, Anti-inflammatory, Synthetic and Natural Compound Bioanalysis.<br />
<br />
+1-508-281-6660<br />
blservices@brunswicklabs.com<br />
200 Turnpike Road, Southborough, MA 01772, USA<br />
<br />
* Bioavailability, BioAbsorption, and BioUptake study via Caco-2 human intestinal cells<br />
* Anti-inflammatory: LOX, COX, TNF-alpha, NFkB, Interleukins (ILs), and PGE2 as biomarkers<br />
* Oxidative Stress Analysis for biological samples<br />
* Antioxidation effect in a biological system: Nrf2, Cellular Antioxidant Assay (CAA) <br />
* Diabetes and Weight Management: insulin secretion, insulin receptor activity, glucose uptake, glucose metabolism, and carbohydrate digestion as biomarkers<br />
* Detoxification and Liver Function: Phase I and Phase II liver enzymes, liver function biomakers in serum<br />
* Energy metabolism investigation via human cells <br />
* Anti-cancer Function evaluation: cancer cell viability, proliferation, apoptosis, and invasion as biomarkers <br />
* Anti-aging Assays: SIRT-1, telomerase activity as biomarkers<br />
* Preclinical Investigations for Skin Care Products: UV protection, melanin (age spot) inhibition, anti-aging, anti-inflammatory<br />
<br />
==[http://biotoxsciences.com/In_Vitro_Services BioToxSciences]==<br />
http://biotoxsciences.com/In_Vitro_Services<br />
<br />
Based in San Diego, they have a range of in-vitro functional assays<br />
<br />
==Other CROs==<br />
* [http://www.alfa-chemistry.com Alfa Chemistry]<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.bocsci.com BOC Sciences]Drug Discovery <br />
* [http://www.creative-peptides.com Creative Peptides]peptide<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs<br />
* [http://www.creative-biogene.com/ Creative Biogene] Transfected Stable Cell Lines<br />
* [http://www.creative-bioarray.com/ Creative Bioarray] Human Umbilical Cord Primary Cells<br />
<br />
== CRO sourcing services ==<br />
* [https://www.scienceexchange.com]<br />
* [https://www.assaydepot.com]<br />
<br />
https://www.genoway.com/services/catalog-models/mouse-knockouts.htm?utm_source=emailing&utm_medium=email&utm_content=01122015&utm_campaign=01122015</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=9880Contract Research Organizations2017-01-25T17:03:36Z<p>Matthew O'Meara: /* Eurofins Panlabs */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They are routinely used by Henry Lin, Matthew O'Meara, and Josh Pottel (2013-2017) and they gave reasonable results at reasonable prices. Note the bulk order discount is for all of UCSF, so no need to try to make large orders.<br />
<br />
The shoichet lab contact there has been (01/17):<br />
John Vu, phone #: 510 227 9213, email: JohnVu@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
In particular they have a protease panel covering over 70 proteases and can possibly develop further targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
3,500 minimum order size e.g. 1 compound at 5 receptors at 10 doses each<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==[http://www.cyprotex.com/toxicology Cyprotex]==<br />
Cyprotex is a contract research organization specializing in preclinical ADME-Tox with offices in the UK and US.<br />
<br />
Permeability & Transporters<br />
* Caco-2 permeability<br />
* Transporter interactions<br />
* PAMPA-GI and PAMPA-BBB<br />
* MDCK and MDR1-MDCK<br />
* Transdermal absorption<br />
* Intranasal absorption<br />
<br />
Distribution - reversible/time dependent<br />
* Plasma protein binding<br />
* Whole blood binding<br />
* Blood to plasma ratio<br />
* Brain tissue binding<br />
* Microsomal binding<br />
<br />
Metabolism<br />
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood<br />
* Metabolite profiling and identification<br />
* Reaction phenotyping<br />
* CYP inhibition<br />
* UGT inhibition<br />
* MAO inhibition<br />
* CYP induction<br />
* PXR and AhR nuclear <br />
<br />
receptor activation<br />
* 3D microtissues<br />
<br />
==[http://www.brunswicklabs.com/biological-analysis Brunswick Labs]==<br />
Brunswick Laboratories is an independent, full-service bioanalytical laboratory specializing in the science of Antioxidants, Oxidative Stress, Anti-inflammatory, Synthetic and Natural Compound Bioanalysis.<br />
<br />
+1-508-281-6660<br />
blservices@brunswicklabs.com<br />
200 Turnpike Road, Southborough, MA 01772, USA<br />
<br />
* Bioavailability, BioAbsorption, and BioUptake study via Caco-2 human intestinal cells<br />
* Anti-inflammatory: LOX, COX, TNF-alpha, NFkB, Interleukins (ILs), and PGE2 as biomarkers<br />
* Oxidative Stress Analysis for biological samples<br />
* Antioxidation effect in a biological system: Nrf2, Cellular Antioxidant Assay (CAA) <br />
* Diabetes and Weight Management: insulin secretion, insulin receptor activity, glucose uptake, glucose metabolism, and carbohydrate digestion as biomarkers<br />
* Detoxification and Liver Function: Phase I and Phase II liver enzymes, liver function biomakers in serum<br />
* Energy metabolism investigation via human cells <br />
* Anti-cancer Function evaluation: cancer cell viability, proliferation, apoptosis, and invasion as biomarkers <br />
* Anti-aging Assays: SIRT-1, telomerase activity as biomarkers<br />
* Preclinical Investigations for Skin Care Products: UV protection, melanin (age spot) inhibition, anti-aging, anti-inflammatory<br />
<br />
==[http://biotoxsciences.com/In_Vitro_Services BioToxSciences]==<br />
http://biotoxsciences.com/In_Vitro_Services<br />
<br />
Based in San Diego, they have a range of in-vitro functional assays<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.bocsci.com BOC Sciences]Drug Discovery <br />
* [http://www.creative-peptides.com Creative Peptides]peptide<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs<br />
* [http://www.creative-biogene.com/ Creative Biogene] Transfected Stable Cell Lines<br />
* [http://www.creative-bioarray.com/ Creative Bioarray] Human Umbilical Cord Primary Cells<br />
<br />
== CRO sourcing services ==<br />
* [https://www.scienceexchange.com]<br />
* [https://www.assaydepot.com]<br />
<br />
https://www.genoway.com/services/catalog-models/mouse-knockouts.htm?utm_source=emailing&utm_medium=email&utm_content=01122015&utm_campaign=01122015</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Gpus&diff=9498Gpus2016-07-01T18:52:49Z<p>Matthew O'Meara: </p>
<hr />
<div>We have 7 GPUs on the cluster. (June 2016). <br />
There is a separate queue gpu.q to manage jobs<br />
<br />
To log in interactively to the gpu queue:<br />
<pre><br />
qlogin -q gpu.q<br />
</pre><br />
<br />
Each gpu is a GeForce GTX 980<br />
<pre><br />
/sbin/lspci | grep -i nvidia<br />
</pre><br />
<br />
Instructions for getting setup for GPU computation: http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux/<br />
<br />
NVidia drivers are installed in /usr/loca/cuda*. To use the 7.5 drivers, make sure these environment variables are set:<br />
<br />
<pre><br />
export PATH=/usr/local/cuda-7.5/bin:$PATH<br />
export LD_LIBRARY_PATH=/usr/local/cuda-7.0/lib64:$LD_LIBRARY_PATH<br />
</pre><br />
<br />
Check that the drivers are installed:<br />
<br />
<pre><br />
cat /proc/driver/nvidia/version<br />
</pre><br />
which should return<br />
<pre><br />
NVRM version: NVIDIA UNIX x86_64 Kernel Module 352.79 Wed Jan 13 16:17:53 PST 2016<br />
GCC version: gcc version 4.4.7 20120313 (Red Hat 4.4.7-16) (GCC)<br />
</pre><br />
<br />
Try compiling and running the sample programs:<br />
<pre><br />
mkdir -p /scratch/$USER/cuda-7.5_samples<br />
cp -r /usr/local/cuda-7.5/samples /scratch/$USER/cuda-7.5_samples<br />
cd /scratch/$USER/cuda-7.5_samples/<br />
make<br />
</pre><br />
<br />
Run the sample program<br />
<pre><br />
/nfs/ge/bin/on-one-gpu - /scratch/$USER/cuda-7.5_samples/bin/x86_64/linux/release/deviceQuery<br />
</pre><br />
<br />
<br />
<br />
Here is a sample script to run amber:<br />
/nfs/work/tbalius/MOR/run_amber/run.pmemd_cuda_wraper.csh<br />
<br />
Here is an excerpt from script<br />
<pre><br />
##########<br />
cat << EOF > qsub.amber.csh<br />
#\$ -S /bin/csh<br />
#\$ -cwd<br />
#\$ -q gpu.q<br />
#\$ -o stdout<br />
#\$ -e stderr<br />
<br />
# export CUDA_VISIBLE_DEVICES="0,1,2,3" <br />
# setenv CUDA_VISIBLE_DEVICES "0,1,2,3"<br />
setenv AMBERHOME /nfs/soft/amber/amber14/ <br />
set amberexe = "/nfs/ge/bin/on-one-gpu - \$AMBERHOME/bin/pmemd.cuda"<br />
##########<br />
</pre><br />
Note that we run the executable with on-one-gpu. <br />
This manages which gpus are used. <br />
<br />
<br />
<br />
<br />
<br />
<br />
If you generate significant output, which is generally but not always true,<br />
it is important to write locally to scratch and then copy things over the network onto the disk. <br />
If you write large amounts of data directly to the NFS disk it can cause problems for others.<br />
<br />
[[Category:GPU]]<br />
[[Category:Internal]]</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=9311Contract Research Organizations2016-03-08T17:18:04Z<p>Matthew O'Meara: /* INDIGO Biosciences */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
In particular they have a protease panel covering over 70 proteases and can possibly develop further targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
3,500 minimum order size e.g. 1 compound at 5 receptors at 10 doses each<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==[http://www.cyprotex.com/toxicology Cyprotex]==<br />
Cyprotex is a contract research organization specializing in preclinical ADME-Tox with offices in the UK and US.<br />
<br />
Permeability & Transporters<br />
* Caco-2 permeability<br />
* Transporter interactions<br />
* PAMPA-GI and PAMPA-BBB<br />
* MDCK and MDR1-MDCK<br />
* Transdermal absorption<br />
* Intranasal absorption<br />
<br />
Distribution - reversible/time dependent<br />
* Plasma protein binding<br />
* Whole blood binding<br />
* Blood to plasma ratio<br />
* Brain tissue binding<br />
* Microsomal binding<br />
<br />
Metabolism<br />
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood<br />
* Metabolite profiling and identification<br />
* Reaction phenotyping<br />
* CYP inhibition<br />
* UGT inhibition<br />
* MAO inhibition<br />
* CYP induction<br />
* PXR and AhR nuclear <br />
<br />
receptor activation<br />
* 3D microtissues<br />
<br />
==[http://www.brunswicklabs.com/biological-analysis Brunswick Labs]==<br />
Brunswick Laboratories is an independent, full-service bioanalytical laboratory specializing in the science of Antioxidants, Oxidative Stress, Anti-inflammatory, Synthetic and Natural Compound Bioanalysis.<br />
<br />
+1-508-281-6660<br />
blservices@brunswicklabs.com<br />
200 Turnpike Road, Southborough, MA 01772, USA<br />
<br />
* Bioavailability, BioAbsorption, and BioUptake study via Caco-2 human intestinal cells<br />
* Anti-inflammatory: LOX, COX, TNF-alpha, NFkB, Interleukins (ILs), and PGE2 as biomarkers<br />
* Oxidative Stress Analysis for biological samples<br />
* Antioxidation effect in a biological system: Nrf2, Cellular Antioxidant Assay (CAA) <br />
* Diabetes and Weight Management: insulin secretion, insulin receptor activity, glucose uptake, glucose metabolism, and carbohydrate digestion as biomarkers<br />
* Detoxification and Liver Function: Phase I and Phase II liver enzymes, liver function biomakers in serum<br />
* Energy metabolism investigation via human cells <br />
* Anti-cancer Function evaluation: cancer cell viability, proliferation, apoptosis, and invasion as biomarkers <br />
* Anti-aging Assays: SIRT-1, telomerase activity as biomarkers<br />
* Preclinical Investigations for Skin Care Products: UV protection, melanin (age spot) inhibition, anti-aging, anti-inflammatory<br />
<br />
==[http://biotoxsciences.com/In_Vitro_Services BioToxSciences]==<br />
http://biotoxsciences.com/In_Vitro_Services<br />
<br />
Based in San Diego, they have a range of in-vitro functional assays<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs<br />
<br />
== CRO sourcing services ==<br />
* [https://www.scienceexchange.com]<br />
* [https://www.assaydepot.com]<br />
<br />
https://www.genoway.com/services/catalog-models/mouse-knockouts.htm?utm_source=emailing&utm_medium=email&utm_content=01122015&utm_campaign=01122015</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=9276Contract Research Organizations2016-01-19T16:36:07Z<p>Matthew O'Meara: /* GenScript */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
In particular they have a protease panel covering over 70 proteases and can possibly develop further targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==[http://www.cyprotex.com/toxicology Cyprotex]==<br />
Cyprotex is a contract research organization specializing in preclinical ADME-Tox with offices in the UK and US.<br />
<br />
Permeability & Transporters<br />
* Caco-2 permeability<br />
* Transporter interactions<br />
* PAMPA-GI and PAMPA-BBB<br />
* MDCK and MDR1-MDCK<br />
* Transdermal absorption<br />
* Intranasal absorption<br />
<br />
Distribution - reversible/time dependent<br />
* Plasma protein binding<br />
* Whole blood binding<br />
* Blood to plasma ratio<br />
* Brain tissue binding<br />
* Microsomal binding<br />
<br />
Metabolism<br />
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood<br />
* Metabolite profiling and identification<br />
* Reaction phenotyping<br />
* CYP inhibition<br />
* UGT inhibition<br />
* MAO inhibition<br />
* CYP induction<br />
* PXR and AhR nuclear <br />
<br />
receptor activation<br />
* 3D microtissues<br />
<br />
==[http://www.brunswicklabs.com/biological-analysis Brunswick Labs]==<br />
Brunswick Laboratories is an independent, full-service bioanalytical laboratory specializing in the science of Antioxidants, Oxidative Stress, Anti-inflammatory, Synthetic and Natural Compound Bioanalysis.<br />
<br />
+1-508-281-6660<br />
blservices@brunswicklabs.com<br />
200 Turnpike Road, Southborough, MA 01772, USA<br />
<br />
* Bioavailability, BioAbsorption, and BioUptake study via Caco-2 human intestinal cells<br />
* Anti-inflammatory: LOX, COX, TNF-alpha, NFkB, Interleukins (ILs), and PGE2 as biomarkers<br />
* Oxidative Stress Analysis for biological samples<br />
* Antioxidation effect in a biological system: Nrf2, Cellular Antioxidant Assay (CAA) <br />
* Diabetes and Weight Management: insulin secretion, insulin receptor activity, glucose uptake, glucose metabolism, and carbohydrate digestion as biomarkers<br />
* Detoxification and Liver Function: Phase I and Phase II liver enzymes, liver function biomakers in serum<br />
* Energy metabolism investigation via human cells <br />
* Anti-cancer Function evaluation: cancer cell viability, proliferation, apoptosis, and invasion as biomarkers <br />
* Anti-aging Assays: SIRT-1, telomerase activity as biomarkers<br />
* Preclinical Investigations for Skin Care Products: UV protection, melanin (age spot) inhibition, anti-aging, anti-inflammatory<br />
<br />
==[http://biotoxsciences.com/In_Vitro_Services BioToxSciences]==<br />
http://biotoxsciences.com/In_Vitro_Services<br />
<br />
Based in San Diego, they have a range of in-vitro functional assays<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs<br />
<br />
== CRO sourcing services ==<br />
* [https://www.scienceexchange.com]<br />
* [https://www.assaydepot.com]</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=9236Contract Research Organizations2015-11-26T15:14:20Z<p>Matthew O'Meara: Add CRO sourcing services section</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==[http://www.cyprotex.com/toxicology Cyprotex]==<br />
Cyprotex is a contract research organization specializing in preclinical ADME-Tox with offices in the UK and US.<br />
<br />
Permeability & Transporters<br />
* Caco-2 permeability<br />
* Transporter interactions<br />
* PAMPA-GI and PAMPA-BBB<br />
* MDCK and MDR1-MDCK<br />
* Transdermal absorption<br />
* Intranasal absorption<br />
<br />
Distribution - reversible/time dependent<br />
* Plasma protein binding<br />
* Whole blood binding<br />
* Blood to plasma ratio<br />
* Brain tissue binding<br />
* Microsomal binding<br />
<br />
Metabolism<br />
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood<br />
* Metabolite profiling and identification<br />
* Reaction phenotyping<br />
* CYP inhibition<br />
* UGT inhibition<br />
* MAO inhibition<br />
* CYP induction<br />
* PXR and AhR nuclear <br />
<br />
receptor activation<br />
* 3D microtissues<br />
<br />
==[http://www.brunswicklabs.com/biological-analysis Brunswick Labs]==<br />
Brunswick Laboratories is an independent, full-service bioanalytical laboratory specializing in the science of Antioxidants, Oxidative Stress, Anti-inflammatory, Synthetic and Natural Compound Bioanalysis.<br />
<br />
+1-508-281-6660<br />
blservices@brunswicklabs.com<br />
200 Turnpike Road, Southborough, MA 01772, USA<br />
<br />
* Bioavailability, BioAbsorption, and BioUptake study via Caco-2 human intestinal cells<br />
* Anti-inflammatory: LOX, COX, TNF-alpha, NFkB, Interleukins (ILs), and PGE2 as biomarkers<br />
* Oxidative Stress Analysis for biological samples<br />
* Antioxidation effect in a biological system: Nrf2, Cellular Antioxidant Assay (CAA) <br />
* Diabetes and Weight Management: insulin secretion, insulin receptor activity, glucose uptake, glucose metabolism, and carbohydrate digestion as biomarkers<br />
* Detoxification and Liver Function: Phase I and Phase II liver enzymes, liver function biomakers in serum<br />
* Energy metabolism investigation via human cells <br />
* Anti-cancer Function evaluation: cancer cell viability, proliferation, apoptosis, and invasion as biomarkers <br />
* Anti-aging Assays: SIRT-1, telomerase activity as biomarkers<br />
* Preclinical Investigations for Skin Care Products: UV protection, melanin (age spot) inhibition, anti-aging, anti-inflammatory<br />
<br />
==[http://biotoxsciences.com/In_Vitro_Services BioToxSciences]==<br />
http://biotoxsciences.com/In_Vitro_Services<br />
<br />
Based in San Diego, they have a range of in-vitro functional assays<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs<br />
<br />
== CRO sourcing services ==<br />
* [https://www.scienceexchange.com]<br />
* [https://www.assaydepot.com]</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=9231Contract Research Organizations2015-11-16T16:59:44Z<p>Matthew O'Meara: /* Other CROs */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==[http://www.cyprotex.com/toxicology Cyprotex]==<br />
Cyprotex is a contract research organization specializing in preclinical ADME-Tox with offices in the UK and US.<br />
<br />
Permeability & Transporters<br />
* Caco-2 permeability<br />
* Transporter interactions<br />
* PAMPA-GI and PAMPA-BBB<br />
* MDCK and MDR1-MDCK<br />
* Transdermal absorption<br />
* Intranasal absorption<br />
<br />
Distribution - reversible/time dependent<br />
* Plasma protein binding<br />
* Whole blood binding<br />
* Blood to plasma ratio<br />
* Brain tissue binding<br />
* Microsomal binding<br />
<br />
Metabolism<br />
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood<br />
* Metabolite profiling and identification<br />
* Reaction phenotyping<br />
* CYP inhibition<br />
* UGT inhibition<br />
* MAO inhibition<br />
* CYP induction<br />
* PXR and AhR nuclear <br />
<br />
receptor activation<br />
* 3D microtissues<br />
<br />
==[http://www.brunswicklabs.com/biological-analysis Brunswick Labs]==<br />
Brunswick Laboratories is an independent, full-service bioanalytical laboratory specializing in the science of Antioxidants, Oxidative Stress, Anti-inflammatory, Synthetic and Natural Compound Bioanalysis.<br />
<br />
+1-508-281-6660<br />
blservices@brunswicklabs.com<br />
200 Turnpike Road, Southborough, MA 01772, USA<br />
<br />
* Bioavailability, BioAbsorption, and BioUptake study via Caco-2 human intestinal cells<br />
* Anti-inflammatory: LOX, COX, TNF-alpha, NFkB, Interleukins (ILs), and PGE2 as biomarkers<br />
* Oxidative Stress Analysis for biological samples<br />
* Antioxidation effect in a biological system: Nrf2, Cellular Antioxidant Assay (CAA) <br />
* Diabetes and Weight Management: insulin secretion, insulin receptor activity, glucose uptake, glucose metabolism, and carbohydrate digestion as biomarkers<br />
* Detoxification and Liver Function: Phase I and Phase II liver enzymes, liver function biomakers in serum<br />
* Energy metabolism investigation via human cells <br />
* Anti-cancer Function evaluation: cancer cell viability, proliferation, apoptosis, and invasion as biomarkers <br />
* Anti-aging Assays: SIRT-1, telomerase activity as biomarkers<br />
* Preclinical Investigations for Skin Care Products: UV protection, melanin (age spot) inhibition, anti-aging, anti-inflammatory<br />
<br />
==[http://biotoxsciences.com/In_Vitro_Services BioToxSciences]==<br />
http://biotoxsciences.com/In_Vitro_Services<br />
<br />
Based in San Diego, they have a range of in-vitro functional assays<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=9230Contract Research Organizations2015-11-16T16:59:26Z<p>Matthew O'Meara: </p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==[http://www.cyprotex.com/toxicology Cyprotex]==<br />
Cyprotex is a contract research organization specializing in preclinical ADME-Tox with offices in the UK and US.<br />
<br />
Permeability & Transporters<br />
* Caco-2 permeability<br />
* Transporter interactions<br />
* PAMPA-GI and PAMPA-BBB<br />
* MDCK and MDR1-MDCK<br />
* Transdermal absorption<br />
* Intranasal absorption<br />
<br />
Distribution - reversible/time dependent<br />
* Plasma protein binding<br />
* Whole blood binding<br />
* Blood to plasma ratio<br />
* Brain tissue binding<br />
* Microsomal binding<br />
<br />
Metabolism<br />
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood<br />
* Metabolite profiling and identification<br />
* Reaction phenotyping<br />
* CYP inhibition<br />
* UGT inhibition<br />
* MAO inhibition<br />
* CYP induction<br />
* PXR and AhR nuclear <br />
<br />
receptor activation<br />
* 3D microtissues<br />
<br />
==[http://www.brunswicklabs.com/biological-analysis Brunswick Labs]==<br />
Brunswick Laboratories is an independent, full-service bioanalytical laboratory specializing in the science of Antioxidants, Oxidative Stress, Anti-inflammatory, Synthetic and Natural Compound Bioanalysis.<br />
<br />
+1-508-281-6660<br />
blservices@brunswicklabs.com<br />
200 Turnpike Road, Southborough, MA 01772, USA<br />
<br />
* Bioavailability, BioAbsorption, and BioUptake study via Caco-2 human intestinal cells<br />
* Anti-inflammatory: LOX, COX, TNF-alpha, NFkB, Interleukins (ILs), and PGE2 as biomarkers<br />
* Oxidative Stress Analysis for biological samples<br />
* Antioxidation effect in a biological system: Nrf2, Cellular Antioxidant Assay (CAA) <br />
* Diabetes and Weight Management: insulin secretion, insulin receptor activity, glucose uptake, glucose metabolism, and carbohydrate digestion as biomarkers<br />
* Detoxification and Liver Function: Phase I and Phase II liver enzymes, liver function biomakers in serum<br />
* Energy metabolism investigation via human cells <br />
* Anti-cancer Function evaluation: cancer cell viability, proliferation, apoptosis, and invasion as biomarkers <br />
* Anti-aging Assays: SIRT-1, telomerase activity as biomarkers<br />
* Preclinical Investigations for Skin Care Products: UV protection, melanin (age spot) inhibition, anti-aging, anti-inflammatory<br />
<br />
==[http://biotoxsciences.com/In_Vitro_Services BioToxSciences]==<br />
http://biotoxsciences.com/In_Vitro_Services<br />
<br />
Based in San Diego, they have a range of in-vitro functional assays<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=9227Contract Research Organizations2015-11-10T00:53:43Z<p>Matthew O'Meara: /* Add Brunswick Labs*/</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==[http://www.cyprotex.com/toxicology Cyprotex]==<br />
Cyprotex is a contract research organization specializing in preclinical ADME-Tox with offices in the UK and US.<br />
<br />
Permeability & Transporters<br />
* Caco-2 permeability<br />
* Transporter interactions<br />
* PAMPA-GI and PAMPA-BBB<br />
* MDCK and MDR1-MDCK<br />
* Transdermal absorption<br />
* Intranasal absorption<br />
<br />
Distribution - reversible/time dependent<br />
* Plasma protein binding<br />
* Whole blood binding<br />
* Blood to plasma ratio<br />
* Brain tissue binding<br />
* Microsomal binding<br />
<br />
Metabolism<br />
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood<br />
* Metabolite profiling and identification<br />
* Reaction phenotyping<br />
* CYP inhibition<br />
* UGT inhibition<br />
* MAO inhibition<br />
* CYP induction<br />
* PXR and AhR nuclear <br />
<br />
receptor activation<br />
* 3D microtissues<br />
<br />
==[http://www.brunswicklabs.com/biological-analysis Brunswick Labs]==<br />
Brunswick Laboratories is an independent, full-service bioanalytical laboratory specializing in the science of Antioxidants, Oxidative Stress, Anti-inflammatory, Synthetic and Natural Compound Bioanalysis.<br />
<br />
+1-508-281-6660<br />
blservices@brunswicklabs.com<br />
200 Turnpike Road, Southborough, MA 01772, USA<br />
<br />
* Bioavailability, BioAbsorption, and BioUptake study via Caco-2 human intestinal cells<br />
* Anti-inflammatory: LOX, COX, TNF-alpha, NFkB, Interleukins (ILs), and PGE2 as biomarkers<br />
* Oxidative Stress Analysis for biological samples<br />
* Antioxidation effect in a biological system: Nrf2, Cellular Antioxidant Assay (CAA) <br />
* Diabetes and Weight Management: insulin secretion, insulin receptor activity, glucose uptake, glucose metabolism, and carbohydrate digestion as biomarkers<br />
* Detoxification and Liver Function: Phase I and Phase II liver enzymes, liver function biomakers in serum<br />
* Energy metabolism investigation via human cells <br />
* Anti-cancer Function evaluation: cancer cell viability, proliferation, apoptosis, and invasion as biomarkers <br />
* Anti-aging Assays: SIRT-1, telomerase activity as biomarkers<br />
* Preclinical Investigations for Skin Care Products: UV protection, melanin (age spot) inhibition, anti-aging, anti-inflammatory<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=9226Contract Research Organizations2015-11-10T00:44:41Z<p>Matthew O'Meara: /* Add Cyprotex */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==[http://www.cyprotex.com/toxicology Cyprotex]==<br />
Cyprotex is a contract research organization specializing in preclinical ADME-Tox.<br />
<br />
Permeability & Transporters<br />
* Caco-2 permeability<br />
* Transporter interactions<br />
* PAMPA-GI and PAMPA-BBB<br />
* MDCK and MDR1-MDCK<br />
* Transdermal absorption<br />
* Intranasal absorption<br />
<br />
Distribution - reversible/time dependent<br />
* Plasma protein binding<br />
* Whole blood binding<br />
* Blood to plasma ratio<br />
* Brain tissue binding<br />
* Microsomal binding<br />
<br />
Metabolism<br />
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood<br />
* Metabolite profiling and identification<br />
* Reaction phenotyping<br />
* CYP inhibition<br />
* UGT inhibition<br />
* MAO inhibition<br />
* CYP induction<br />
* PXR and AhR nuclear <br />
<br />
receptor activation<br />
* 3D microtissues<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=9225Contract Research Organizations2015-11-05T04:20:45Z<p>Matthew O'Meara: /* Absorption Systems */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=9224Contract Research Organizations2015-11-05T04:20:13Z<p>Matthew O'Meara: /* HD Biosciences */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. We work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8247Contract Research Organizations2015-02-04T12:33:15Z<p>Matthew O'Meara: /* Other CROs */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
*Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
*Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS) <br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8246Contract Research Organizations2015-02-04T12:31:01Z<p>Matthew O'Meara: /* Other CROs */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
*Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
*Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS) <br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8245Contract Research Organizations2015-02-04T12:28:57Z<p>Matthew O'Meara: /* Other CROs */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
*Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
*Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS) <br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8244Contract Research Organizations2015-02-04T04:00:06Z<p>Matthew O'Meara: /* Other CROs */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
*Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
*Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS) <br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8240Contract Research Organizations2015-01-26T21:32:55Z<p>Matthew O'Meara: /* Other CROs */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8239Contract Research Organizations2015-01-26T21:31:21Z<p>Matthew O'Meara: /* PerkinElmer */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8197Contract Research Organizations2014-11-24T18:02:26Z<p>Matthew O'Meara: update zip code for PDSP</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8190Contract Research Organizations2014-11-12T15:59:44Z<p>Matthew O'Meara: Add Cayman Chemical</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here the address to send compounds (good as of 7/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27599<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight<br />
* label the vials with the ID/name and the PDSP# assigned<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8188Contract Research Organizations2014-11-11T18:17:14Z<p>Matthew O'Meara: Add FluoFarma</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here the address to send compounds (good as of 7/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27599<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight<br />
* label the vials with the ID/name and the PDSP# assigned<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells.<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8182Contract Research Organizations2014-11-10T18:56:39Z<p>Matthew O'Meara: Add Sora Labs</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here the address to send compounds (good as of 7/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27599<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight<br />
* label the vials with the ID/name and the PDSP# assigned<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they have can do nuclear hormone assay.<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8174Contract Research Organizations2014-11-07T02:02:56Z<p>Matthew O'Meara: Add INDIGO Biosciences</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here the address to send compounds (good as of 7/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27599<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight<br />
* label the vials with the ID/name and the PDSP# assigned<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they have can do nuclear hormone assay.<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8148Contract Research Organizations2014-10-29T12:38:45Z<p>Matthew O'Meara: Add Eurofins contact</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here the address to send compounds (good as of 7/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27599<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight<br />
* label the vials with the ID/name and the PDSP# assigned<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8147Contract Research Organizations2014-10-28T20:05:45Z<p>Matthew O'Meara: Add InvivoGen</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here the address to send compounds (good as of 7/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27599<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight<br />
* label the vials with the ID/name and the PDSP# assigned<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8146Contract Research Organizations2014-10-28T19:57:44Z<p>Matthew O'Meara: change attn for PDSP</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here the address to send compounds (good as of 7/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27599<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight<br />
* label the vials with the ID/name and the PDSP# assigned<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8103Contract Research Organizations2014-10-07T16:42:25Z<p>Matthew O'Meara: Add GenScript</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here the address to send compounds (good as of 7/2014)<br />
<br />
PDSP<br />
attn Flor Sassa<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27599<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight<br />
* label the vials with the ID/name and the PDSP# assigned<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in Transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in Transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8016Contract Research Organizations2014-09-08T20:15:49Z<p>Matthew O'Meara: /* PDSP */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here the address to send compounds (good as of 7/2014)<br />
<br />
PDSP<br />
attn Flor Sassa<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27599<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight<br />
* label the vials with the ID/name and the PDSP# assigned<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in Transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in Transporters, based in the Bay Area.<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=8015Contract Research Organizations2014-09-08T20:15:20Z<p>Matthew O'Meara: /* PDSP */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here the address to send compounds (good as of 7/2014)<br />
<br />
PDSP<br />
attn Flor Sassa<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27599<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
Shoichet Lab<br />
project name<br />
compound id, amount submitted, molecular weight<br />
label the vials with the ID/name and the PDSP# assigned<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in Transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in Transporters, based in the Bay Area.<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.absorption.com Absorption Biosystems]</div>Matthew O'Mearahttp://wiki.docking.org/index.php?title=Assaying_Compound_Activity&diff=8014Assaying Compound Activity2014-09-02T15:23:13Z<p>Matthew O'Meara: Reorganize testing compounds with CRO</p>
<hr />
<div>Depending on the project, assaying compound activity typically involves acquiring the compound and then getting it tested either in house or sending it out somewhere to be tested. This page details some of the common tasks and considerations in this process. Note, this information is somewhat specific to the Shoichet lab at UCSF.<br />
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=Buying Compounds=<br />
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==Identifying Compounds to Buy==<br />
Depending on the project, compounds may have different requirements<br />
*Requirements for in vitro testing<br />
** Purity: If possible get the compounds at 95% or greater purity even if it costs 100$ or 200$ more. If it's tested to be active but has low purity, it will likely need to be re-purified and then tested.<br />
** Aggregation: Check the compound with the aggregator advisor (advisor.bkslab.org) and if it's close to or known to be an aggregator (indications include uM nonspecific activity, logP great than 3 or actually shown to be an aggregator through appropriate controls) then either skip the compound or plan on doing aggregation controls, e.g. testing for detergent sensitive nonspecific activity, determine particle formation using DLS, or perform the assay with/without detergent (and just detergent controls).<br />
** Amount: try to get 10mg if possible, but if it's very expensive you can get less. If you're sending it to a CRO sending it in solution usually requires less compound. If you're planning on further controls (e.g. for purity, aggregation), make sure to get enough.<br />
** Note the solubility (e.g. water, DMSO, etc.)<br />
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*Requirements for in vivo testing<br />
** Check pharmacokinetics<br />
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==Finding Vendors==<br />
The easiest way to find vendors is through the ZINC portal. Once you login, go to Manage Carts in the upper right and then create new cart, where you put in a list of smiles or zinc ids. Once you've verified these are the right compounds, click purchasability report where it lists which compounds are available from which vendors. In selecting vendors keep the following in mind<br />
* Here are some reliable vendors<br />
** AK Sientific (in SF)<br />
** Toronto Research Chemicals<br />
** Sigma Aldrich (sometimes higher prices but reliable)<br />
** Enamine (has a large catalog, in europe)<br />
** ChemBridge (in SF)<br />
** Santa Cruz Biotech (in CA)<br />
* Some vendors are just resellers, which makes them have larger catalogs, but can increase the price and take longer. Though often this is offset by the ease of use and not having to pay multiple shipping and handling costs.<br />
** MolPort (ieva.kluga@molport.com has been the contact as of July 2014)<br />
** EMolecules<br />
** Ambinter<br />
* If possible try to group multiple compounds per vendor to reduce shipping and handling costs<br />
* Sometimes compounds are available from special catalogs<br />
** NCI Platted: 1) Here is a description of the NCI Platted process from there end [[NCI_Platted]]. Look up the NCS identifier in PubChem. 2) submit a request form through their webpage. Contact the industry contacts officer at ucsf (Esteban.Mendoza@ucsf.edu | t: 415-502-1599) to have him sign the "Simple Letter of Agreement". He'll will give you a materials transfer form that you need to fill out.<br />
* Remember that our lab will continue to buy from these vendors so be nice, and inquire if we can get a lab discount<br />
* For each compound record<br />
** ZincID, supplier, supplier product code, molecular weight, purity<br />
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==Ordering Compounds==<br />
* Get quotes either through the webpage or through vendor contacts<br />
* Get Brian to approve the orders costing more than 500USD.<br />
* Forward quotes to Yvonne or whoever is doing the ordering <br />
*** Be cognizant of the hours the orderer works, sometimes they share time with other labs<br />
*** the quote should including the zincid, vendor, vendor id, amount, and price<br />
*** lookup the project [[grant number]] (or ask Brian),<br />
*** a shipping address<br />
*** whose project this is for <br />
*** who should receive the compounds<br />
*** indicate if the order should be rushed (unless necessary, rushed orders should be avoided as they are generally much more expensive)<br />
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==Testing Compounds with CRO==<br />
*Quote administration<br />
** If the vendor is not in the BearBuy system, they will need to fill out a form that Yvonne can provide<br />
** Get a quote from the company and<br />
** With the quote, get a PO number<br />
** Give the PO number to the vendor when placing the order<br />
** The vendor will then give an Invoice that can go directly to the UCSF Accounts Payable department (COapmail@ucsf.edu) and they will pay the vendor.<br />
*Sending compounds<br />
** Provide the courier (e.g. FedEx) with the address and full name and telephone number of the person who will receive it.<br />
** Indicate with the vendor if the order should be rushed (unless necessary, rushed orders should be avoided as they are generally much more expensive)<br />
** If the supply of the compound is limited, often less is required if it is sent in solution, but it is easier and more stable to send powder, so check with the assay vendor<br />
* Compound testing<br />
** For the given receptor/ligand pair check the known activities to help guide where to start testing.<br />
** If possible, start with a few high concentration (e.g. 2 replicates @ 20 uM) "primary" points to see if there is any activity<br />
** If there is some activity follow up with a 5-10 point dose response curve reducing by half log or 1/3 at each step (where the highest concentrations will depend on the activity of the primary assay).<br />
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[[Category:Tutorials]]</div>Matthew O'Meara