User talk:Frodo
todo
- Keep track of endogenous ligand for each protein
http://zinc15.docking.org/substances/subsets/fda+biogenic/
http://zinc15.docking.org/subclasses/phosphatase/substances/subsets/biogenic/
http://zinc15.docking.org/substances/subsets/biogenic/?genes-any-sub_class_name=GPCR-A&predictions-any-major_class_name=ion%20channel
http://zinc15.docking.org/substances/subsets/biogenic/?genes-any-sub_class_name=GPCR-A&genes-any-major_class_name=ion%20channel
http://zinc15.docking.org/substances/subsets/biogenic/having/rings/subsets/triple/
http://zinc15.docking.org/genes/MCHR2/targets/ http://zinc15.docking.org/substances/subsets/world+natural-products/ http://zinc15.docking.org/genes/having/no-activities/subsets/1uM/?related.purchasability=for-sale&num_substances-ge=1 http://zinc15.docking.org/genes/having/no-activities/subsets/1uM/?related.purchasability=for-sale&num_substances-ge=1
http://zinc15.docking.org/genes/APLNR/substances/subsets/for-sale/table.html
http://zinc15.docking.org/genes/APLNR/substances/subsets/for-sale/
http://zinc15.docking.org/genes/subsets/gpcra/having/no-activities/subsets/100nM/?num_substances-ge=1
http://zinc15.docking.org/genes/subsets/gpcra/having/no-activities/subsets/1uM/
http://zinc15.docking.org/genes/subsets/gpcra/having/activities/?related.affinity-lt=6&num_purchasable=1&num_substances-gt=0
5HT ligands, colored by endogenous ligand
http://zinc15.docking.org/genes/HTR1D/substances/?highlight=5-HT&ecfp4_fp-tanimoto=NCCc1c%5BnH%5Dc2ccc%28O%29cc12
sorted by affinity....
http://zinc15.docking.org/genes/HTR1D/activities/?highlight=5-HT&substance.ecfp4_fp-tanimoto=NCCc1c%5BnH%5Dc2ccc%28O%29cc12
alter user zincfree set search_path = "$user", free, public;
http://zinc15.docking.org/substances/subsets/world/having/no-genes+no-predictions/ http://zinc15.docking.org/substances/subsets/world/having/no-genes+predictions/ http://zinc15.docking.org/substances/subsets/world/having/no-genes/ http://zinc15.docking.org/rings/indole/substances/subsets/world/having/no-genes/ http://zinc15.docking.org/substances/subsets/world/having/patterns/subsets/pains/?sort=no http://zinc15.docking.org/substances/subsets/aggregators/having/trials/ http://zinc15.docking.org/substances/subsets/endogenous/having/patterns/subsets/pains/?sort=no (lots of incorrectly curated) update substance as s set added_on = t.up_date from tempupdate as t where t.sub_id = s.sub_id;
so everything is running on Tau all started in a screen as www called sea-transporters or something there is a single startup script that starts the backend application server as well as the even more backend worker server first you need to source /nfs/soft/www/apps/sea/transporters/env.csh then you can simply run "run-sea-server.sh" however I should make it shut down older servers.. doesn't do that yet BUT the PIDs of the other two servers are written to /nfs/soft/www/apps/sea/transporters/var/seaserver/run so to restart: kill relevant PIDs, then call run-sea-server.sh oh and last last thing, you can clear jobs out by removing their directories from /nfs/soft/www/apps/sea/transporters/var/seaserver/queue/jobs/
tunneling:
ssh -p 22 -L 1080:sgehead.bkslab.org:22 portal.bkslab.org -N scp -P 1080 om.smi xyz@localhost:/raid6/tmp/xyz om.smi
My todo list:
controlling vms
- ssh vmware1.(domain) -l root
- vim-cmd vmsvc/getallvms
- vim-cmd vmsvc/power.on 864
ZINC
- broken - http://zinc12.docking.org/substance/3850657
- C04798508 and C13952160 are the same. many more.
- metal detection in dock blaster. correct treatment of hi library
- 17005395 has charge -1 and 6565555 has charge -1
Blaster
From Oliv: Here are some comments on Dockblaster, which I received as feedback from non-experienced users. It seems that the results page is hard to interpret:
- it is not clear to most people what the 4 schemes (coarse/finer/polarized/Amber) mean and what they should use for docking - the bug that rank and rmsds do not appear in most cases is confusing. Rank and rmsds should also be labeled. - Instead of "Browse subset 12" one could write "Click here for a list of the best 100 molecules" - The results (what people want!) are well hidden at the bottom of the page. Maybe one could give the people only the rec.crg file, eel1/mol2 files? At a more prominent place of the page?
SARAH: hi john- just noticed that indole in the l99a binders set looked funny, so i checked the mol2 files out and ref1 is incorrect; the double bond is in the wrong place. ref2 is the correct form of the molecule. the zinc id is C14516984.
I've had a few goes now with Dockblaster on a couple of targets but am having problems with some Calcium-dependant phospholipases in which the catalytic Ca++ is not being included in rec.pdb . First up I used a couple of structures from our group (e.g. I kqu 1j1a,) but in both cases the calcium doesn't get included. I then tried to prep the protein myself and submit those to Dockblaster but the same problem recurred. Thinking it might just be our structures just this morning I used some other workers PLA2 structure (1DB5 Dockblaster ID #38751) and it also doesn't include the Ca. By comparison a test run with thermolysin (5TLN Dockblaster run # #38752) included it's
Ryan writes: I'm finding many groups that are +2 when Marvin is sure they are 0, maybe sometimes +1. I'm including SMILES strings which hopefully are helpful to see what I'm talking about. I think part of the problem, or maybe the reason things are okay and I'm crazy, is that when you look at the ZINC page
http://zinc12.docking.org/substance/07667606
The benzimidazole group is drawn with all single bonds on the 5-ring, but when you copy/paste the smiles into Marvin or another program there are some double bonds. Very strange (or I'm possibly just confused by chemistry again)
O=C1N=[C]2=[C](C=CC=C2)=N1
Some example ZINC codes follow...
07667606 10201533 57765079 01805265 34781275
Another group that seems to have a similar issue:
CN=C1N=[C]2=[C](C=CC=C2)=N1
12323863 17304169 13688743 11635241 20744559
I have an entire docking run that seems to be full of these 2 if you need more examples.
blaster
dhi, 3frj, /raid3/people/mysinger/pxc/dude/species/dhi1/P28845/blasti/3frj/dock NAP cofactor decapitated
hivpr, 1upj, /raid3/people/mysinger/pxc/dude/species/hivpr/Q72874/blasti/1upj/dock asymmetric only half the biological, two ASP are 2.5A apart and both protonated
mtor, /raid3/people/mysinger/pxc/dude/species/mtor/P42345/blasti/*/dock All ligands failed to build, so 0/5 were build automatically
-- metacyc update http://bioinformatics.ai.sri.com/ptools/flatfile-samples/compounds.dat
-- pubchem update (quarterly)
-- cdd update (quarterly)
https://s3.amazonaws.com/cdd-public/cdd-public-structures-20110219230015.sdf.gz
For future downloads, you can visit https://s3.amazonaws.com/cdd-public/ and figure out the current filename from the XML that is displayed.
ZINC
DOCK Blaster
User Support
1135, 1135, 1141
Table 1 & 2
DUD 40
Astex 305
Scrutinizer
autotart
ligand included in target
cofactor, metals handling
jobwatcher
autolaunch clustering on korn
browse calibration results
Results Browser
basic scores and graphs, even if no xtal-lig
flag.pl to flag bad molecules
pattern support
detail page
show and hide toggles
slice and dice. SMARTS filter
General UI
check bookmarking each page
chimera and pymol on mac, linux
pymol finish off top 500
titles, doc links, alts everywhere
CAPTCHA (long term)
usage stats regularly updated
more professional email update message
Miscellaneous
Brenda is at /raid5/backonce/joha/DB3/5_BRENDA2SDF/ORG_BRENDA_MOL_FILES_PREP/brenda_031306.ism mysql is at mysql -u joha -p*secret* -h (brenda-machine-name-ask-jji) brenda wombat is at ~jerome/sets/wombat/wombat_20062/wombat.20062.sdf.gz
left over bumpf from the old main page.
ZINC || Commercially available compounds || zinc.docking.org
Ligands for my target
- Category:Covalent
- Hit picking party || DOCK 3.7
- DOCK || Our molecular docking software || Latest are DOCK 3.7 and DOCK 6.6
- DOCK Blaster || A public access service for docking screens || blaster.docking.org
- DUDE and DUD || Benchmarks for docking|| dude.docking.org/generate
- HEI || Substrate discovery and function ID || hei.docking.org metabolites.docking.org
Targets for my ligand(s)
- SEA || Similarity Ensemble Approach || Drug repurposing, target ID
- Tutorials
- Assaying Compound Activity
- Topics
- Categories
- Roles
- Article type
- Attributes
- Software
- Databases
- Free || Free to some || Commercial