User talk:Frodo: Difference between revisions

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matt's thing
SEA16
http://sea16.ucsf.bkslab.org/custom/search/target_vs_target?library=chembl_10uM&target_id=SC6A3_HUMAN+5&query_id=SC6A4_HUMAN+5&rank_cutoff=50


  http://sea16.ucsf.bkslab.org/custom/search/target_vs_target?library=chembl_10uM&target_id=SC6A3_HUMAN+5&query_id=SC6A4_HUMAN+5&rank_cutoff=50
Supplier codes and ZINC IDs for list of zinc ids where sold by specific vendors:
  curl 'http://zinc15.docking.org/catitems.txt' -F "catalog-has-short_name-in=enamine sial" -F zinc_id-in=@zincids -F sort=no -F count=all
 
ZINC IDs and all catalogs selling them where at least one catalog is in a specific list of vendors:
curl 'http://zinc15.docking.org/substances.txt:zinc_id+catalogs' -F "catalogs-any-short_name-in=enamine sial" -F zinc_id-in=@zincids  -F sort=no -F count=all


ZINC IDs where catalog in a specific list of vendors:
curl 'http://zinc15.docking.org/substances.txt:zinc_id' -F "catalogs-any-short_name-in=enamine sial" -F zinc_id-in=@zincids  -F sort=no -F count=all


Note: -F sort=no makes the query not sort by ZINC ID, should be slightly faster but safe to turn off


Note: -F count=all returns all results from the query, can also be any integer to take only that many (can be combined with -F page=N to get a later slice)


Compounds recognized by transporters that look like aspirin
Compounds recognized by transporters that look like aspirin
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as above, with smiles:
as above, with smiles:
  htp://zinc15.docking.org/genes/SLC6A4/substances.json:zinc_id+rings
  htp://zinc15.docking.org/genes/SLC6A4/substances.json:zinc_id+rings
= todo =
* Keep track of endogenous ligand for each protein
* bioisosteric substitution
* curate patterns
* clean up rings
* loading
* nplike, bioactive like
* chembl20, all cmpds also target free
*
update substance as s set added_on = t.up_date from tempupdate  as t where t.sub_id = s.sub_id;
<pre>
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/
</pre>
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


{{TOCright}}
{{TOCright}}
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  - Instead of "Browse subset 12" one could write "Click here for a list of the best 100 molecules"
  - 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?
  - 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.
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
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 =  
= blaster =  
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mtor, /raid3/people/mysinger/pxc/dude/species/mtor/P42345/blasti/*/dock
mtor, /raid3/people/mysinger/pxc/dude/species/mtor/P42345/blasti/*/dock
All ligands failed to build, so 0/5 were build automatically
All ligands failed to build, so 0/5 were build automatically


-- metacyc update
-- metacyc update
http://bioinformatics.ai.sri.com/ptools/flatfile-samples/compounds.dat
http://bioinformatics.ai.sri.com/ptools/flatfile-samples/compounds.dat


-- pubchem update (quarterly)
-- pubchem update (quarterly)
-- cdd update (quarterly)
-- cdd update (quarterly)


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https://s3.amazonaws.com/cdd-public/ and figure out the current
https://s3.amazonaws.com/cdd-public/ and figure out the current
filename from the XML that is displayed.
filename from the XML that is displayed.
= ZINC =


= DOCK Blaster =  
= DOCK Blaster =  
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[[Category:jji]]
[[Category:jji]]
[[Category:Info]]
[[Category:Info]]


left over bumpf from the old main page.  
left over bumpf from the old main page.  

Revision as of 23:11, 12 February 2016

SEA16 

http://sea16.ucsf.bkslab.org/custom/search/target_vs_target?library=chembl_10uM&target_id=SC6A3_HUMAN+5&query_id=SC6A4_HUMAN+5&rank_cutoff=50

Supplier codes and ZINC IDs for list of zinc ids where sold by specific vendors: 

curl 'http://zinc15.docking.org/catitems.txt' -F "catalog-has-short_name-in=enamine sial" -F zinc_id-in=@zincids -F sort=no -F count=all

ZINC IDs and all catalogs selling them where at least one catalog is in a specific list of vendors: 

curl 'http://zinc15.docking.org/substances.txt:zinc_id+catalogs' -F "catalogs-any-short_name-in=enamine sial" -F zinc_id-in=@zincids  -F sort=no -F count=all

ZINC IDs where catalog in a specific list of vendors: 

curl 'http://zinc15.docking.org/substances.txt:zinc_id' -F "catalogs-any-short_name-in=enamine sial" -F zinc_id-in=@zincids  -F sort=no -F count=all

Note: -F sort=no makes the query not sort by ZINC ID, should be slightly faster but safe to turn off

Note: -F count=all returns all results from the query, can also be any integer to take only that many (can be combined with -F page=N to get a later slice)

Compounds recognized by transporters that look like aspirin 

http://zinc15.docking.org/majorclasses/transporter/substances/?highlight=aspirin&ecfp4_fp-tanimoto-40=CC%28%3DO%29Oc1ccccc1C%28%3DO%29O

Compounds that have names in ZINC 

http://zinc15.docking.org/substances/?substance-hasany=name_entries

Names of all rings of all SERT ligands, in a file 

http://zinc15.docking.org/genes/SLC6A4/substances.txt:zinc_id+rings&count=all

as above, with smiles: 

htp://zinc15.docking.org/genes/SLC6A4/substances.json:zinc_id+rings

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

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.

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

Targets for my ligand(s)

  • SEA || Similarity Ensemble Approach || Drug repurposing, target ID

Introduction, overview, navigation, help

Everything else

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