Getting started with DOCK 3.7: Difference between revisions
No edit summary |
|||
Line 40: | Line 40: | ||
= Test 1: Basic tests = | = Test 1: Basic tests = | ||
This will tell you quick what you forgot to install or if there is any obvious problem with your installation. If you can pass the tests, you are ready to proceed to the following steps. | This will tell you quick what you forgot to install or if there is any obvious problem with your installation. If you can pass the tests, you are ready to proceed to the following steps. | ||
cd $DOCKBASE/test | cd ~/$DOCKBASE/test | ||
./all-test.sh | ./all-test.sh | ||
This should run about 10-30 minutes depending on your hardware, and should either produce clear error messages (work needed) or a clear message that the tests succeeded without problems. | |||
= Test 2: Docking preparation from receptor and ligand alone = | = Test 2: Docking preparation from receptor and ligand alone = | ||
Here we prepare the endogenous human metabolites for docking. | Here we prepare the endogenous human metabolites for docking. | ||
mkdir -p ~/docking/test1 | |||
mkdir -p docking/test1 | |||
cd $DOCKBASE/test/data/xiap/proteins/initial | cd $DOCKBASE/test/data/xiap/proteins/initial | ||
cp rec.pdb xtal-lig.pdb ~/docking/test1/ | cp rec.pdb xtal-lig.pdb ~/docking/test1/ | ||
Line 54: | Line 54: | ||
= Test 3. Prepare library for docking = | = Test 3. Prepare library for docking = | ||
Here we prepare the endogenous human metabolites. | Here we prepare the endogenous human metabolites. | ||
mkdir -p ~/database/testa | |||
mkdir -p database/testa | cd ~/database/testa | ||
cd database/testa | |||
wget http://zinc.docking.org/db/byvendor/hmdbendo/hmdbendo_p0.smi.gz | wget http://zinc.docking.org/db/byvendor/hmdbendo/hmdbendo_p0.smi.gz | ||
gunzip hmdbendo_p0.smi.gz | gunzip hmdbendo_p0.smi.gz | ||
head hmdbendo_p0.smi > top10.smi | |||
dbgen.csh top10.smi | |||
If this succeeds without trouble, try a bigger database: | |||
dbgen.csh hmdbendo_p0.smi | |||
= Test 4. Dock custom library = | = Test 4. Dock custom library = | ||
* | * set up docking in Test 2 above to dock the libraries created in Test 3 above. | ||
* | * step by step instructions. | ||
= Test 5. Run the DUD and DUDE benchmarks and generate statistics = | = Test 5. Run the DUD and DUDE benchmarks and generate statistics to assess how well docking is working = | ||
* [[Download DUD]] | |||
* [[Dock DUD]] | |||
* [[Run analysis tools on DUD]] | |||
* [[Download DUDE]] | |||
* [[Dock DUDE]] | |||
* [[Run analysis tools on DUDE]] | |||
= Test 6. Acquire public library and dock it = | = Test 6. Acquire public library and dock it = | ||
[[ | Use [[ZINC Subset DB2 file locations]] to locate [[mol2db2 format]] libraries of popular subsets until they are available in [[ZINC]] (later in 2014). | ||
= Test 7. Dock starting from PDB code = | = Test 7. Dock starting from PDB code = | ||
* | * [[Run be_blasti]] | ||
* run blastermaster | * run blastermaster (see Test 2 above) | ||
* run docking | * run docking (see test 4 above) | ||
= Test 8. Perform fine-tuned docking run = | |||
== fine tune docking spheres (hot spots) == | |||
* step 1 | |||
* step 2 | |||
* step 3 | |||
= | == fine tune VDW spheres == | ||
* step 1 | |||
* | * step 2 | ||
* | * step 3 | ||
* | |||
* | == fine tune bounding box == | ||
* | * step 1 | ||
* step 2 | |||
* step 3 | |||
== handle ZINC ion and its coordinating residues == | |||
* step 1 | |||
* step 2 | |||
* step 3 | |||
== fine tune electostatics (tarting up) == | |||
* step 1 | |||
* step 2 | |||
* step 3 | |||
== fine tune other features of docking (enumerate) == | |||
* one | |||
* two | |||
* three | |||
Return to [[DOCK 3.7]]. | Return to [[DOCK 3.7]]. |
Revision as of 23:18, 24 February 2014
You want to install the DOCK 3.7 package on your own system, including the entire docking pipeline and database building. These are the notes I made while doing it. Just recommendations. You are free to simply download the software and experiment!
Acquire 3rd party software
- Centos - we use Centos 6.3 or higher, but many other unixes may work. Supported platforms for DOCK 3.7.
- Python - 2.7 series - We do not support the 3.x series, and 2.5 or earlier can also cause problems.
- AMSOL - for atomic charge and desolvation penalty calculations required for database building.
- Omega from OpenEye - for conformation generation required for database building.
- Either PyMol or Chimera for 3D modeling.
- Matplotlib - currently only needed for analysis plots (enrichment)
- MSMS - currently only needed by be_blasti
- rdkit - recommended but currently not essential for the DOCK 3.7 pipeline.
- OGS/GE - queuing system. OpenGridEngine is included in Centos and you do not need to install it separately.
Acquire our software
Here we install a private copy under a user's account. It is easy to generalize this to a global location, e.g. /nfs/software . You can request a license and a copy (free to academics, a bargain for for-profits) at http://dock.compbio.ucsf.edu/Online_licensing/dock_license_application.html. Request DOCK 3.7.
cd mkdir code cd code cp ~xyz/DOCK.tgz . # or get distro from dock.compbio.ucsf.edu website as above tar xzf DOCK.tgz # unpack
set up .cshrc (or .bashrc equivalent)
You need to create something like this, depending on your exact circumstances.
setenv DOCKBASE /raid4/people/mattchu/code/DOCK set path = ($path $DOCKBASE/bin) setenv AMSOLEXE $DOCKBASE/bin/amsol-mod4 setenv OE_DIR /raid3/software/openeye/current alias pymol ~/pymol/pymol if ( $?PYTHONPATH ) then if ( `echo $PYTHONPATH | grep -c 'openeye/python'` == 0 ) then setenv PYTHONPATH $OE_DIR/python:${PYTHONPATH} endif else setenv PYTHONPATH $OE_DIR/python endif
Test 1: Basic tests
This will tell you quick what you forgot to install or if there is any obvious problem with your installation. If you can pass the tests, you are ready to proceed to the following steps.
cd ~/$DOCKBASE/test ./all-test.sh
This should run about 10-30 minutes depending on your hardware, and should either produce clear error messages (work needed) or a clear message that the tests succeeded without problems.
Test 2: Docking preparation from receptor and ligand alone
Here we prepare the endogenous human metabolites for docking.
mkdir -p ~/docking/test1 cd $DOCKBASE/test/data/xiap/proteins/initial cp rec.pdb xtal-lig.pdb ~/docking/test1/ cd ~/docking/test1/ blastermaster -v
Test 3. Prepare library for docking
Here we prepare the endogenous human metabolites.
mkdir -p ~/database/testa cd ~/database/testa wget http://zinc.docking.org/db/byvendor/hmdbendo/hmdbendo_p0.smi.gz gunzip hmdbendo_p0.smi.gz head hmdbendo_p0.smi > top10.smi dbgen.csh top10.smi
If this succeeds without trouble, try a bigger database:
dbgen.csh hmdbendo_p0.smi
Test 4. Dock custom library
- set up docking in Test 2 above to dock the libraries created in Test 3 above.
- step by step instructions.
Test 5. Run the DUD and DUDE benchmarks and generate statistics to assess how well docking is working
Test 6. Acquire public library and dock it
Use ZINC Subset DB2 file locations to locate mol2db2 format libraries of popular subsets until they are available in ZINC (later in 2014).
Test 7. Dock starting from PDB code
- Run be_blasti
- run blastermaster (see Test 2 above)
- run docking (see test 4 above)
Test 8. Perform fine-tuned docking run
fine tune docking spheres (hot spots)
- step 1
- step 2
- step 3
fine tune VDW spheres
- step 1
- step 2
- step 3
fine tune bounding box
- step 1
- step 2
- step 3
handle ZINC ion and its coordinating residues
- step 1
- step 2
- step 3
fine tune electostatics (tarting up)
- step 1
- step 2
- step 3
fine tune other features of docking (enumerate)
- one
- two
- three
Return to DOCK 3.7.