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= application: advisor =  
= application: advisor =  
= Use Case examples =
Create a database of in stock commercially available arylsulfonamides for docking =
api.docking.org/v1/zinc/subset/substances/smiles,sub_id/substance contains c1ccccc1S(=O)(=O)N&catalog.purchasable gt 20
This is created as job # 122334
Now find a upload a structure and docking this library to it
api.docking.org/v1/dock/upload/rec=rec.pdb,lig=xtal-lig.pdb,lib=122334
This is created as job # 556677
Download the docking results for docking on the client
api.docking.org/v1/556677/download/all
Download the arylsulfonamide database created above in db2 format
api.docking.org/v1/122334/download/db2


[[Category:ZINC15]]
[[Category:ZINC15]]

Revision as of 17:42, 8 December 2014

This is a description of the 2015 api to docking.org services. The URL takes one of two forms

1. api.docking.org/vX/application/action/arguments

2. api.docking.org/vX/job_number/action/arguments


Where application is one of: zinc, docking, covalent, decoys, dude, advisor. We take up the arguments of each of these below:

application:docking

Supported actions are: pdb, upload, listpdb, jobs, myjobs

pdb: specify pdb code for automatic (be_blasti) docking

upload: specify receptor and binding site. if binding site not specified, pockets are picked.

list: list all pdb codes supported

jobs: list all recent jobs in system

myjobs: list my recent jobs (based on apikey)


Actions for operating on a docking job

info : display what kind of job it is, when submitted, current status. pickpockets : pick pockets library: specify library for docking


application:covalent

supported actions are: upload, jobs, myjobs

upload: specify receptor and covalent attachment point.

actions for operating on a covalent docking job

info: display what kind of job it is, when submitted, current status library: specify library for docking


application: decoys

Supported actions are: make, get, list

make: make decoys based on uploaded molecules

get: specify gene, get both actives and decoys from chembl for that gene

list: list all genes for which decoys (and actives) are available.

application: zinc

supported actions: upload, download, prepare, subset, hotsubset

upload: upload molecules for standard preparation using zinc pipeline. Libraries uploaded in this way may be used by docking

download: download large custom subset in any format.

prepare: make sure 3D versions of a subset are ready for download (this may take weeks)

subset: create a subset for docking,

hotsubset: prepare covalent docking database


application: advisor

Use Case examples

Create a database of in stock commercially available arylsulfonamides for docking =

api.docking.org/v1/zinc/subset/substances/smiles,sub_id/substance contains c1ccccc1S(=O)(=O)N&catalog.purchasable gt 20

This is created as job # 122334

Now find a upload a structure and docking this library to it

api.docking.org/v1/dock/upload/rec=rec.pdb,lig=xtal-lig.pdb,lib=122334

This is created as job # 556677

Download the docking results for docking on the client

api.docking.org/v1/556677/download/all

Download the arylsulfonamide database created above in db2 format

api.docking.org/v1/122334/download/db2