Api15

This is a description of the 2015 api to docking.org services.

Syntax

The URL takes one of two forms

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

1. api.docking.org/vX/job_number/application/subaction/arguments

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

Applications

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)

Sub-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.

Sub-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.

Subactions for acting on a decoys job

Supported subactions are: download

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

Sub-actions for application: zinc

Supported subactions are: download

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

Upload a structure of unknown function and unknown binding site, identify binding site

api.docking.org/v1/dock/upload/rec=rec.pdb  # implies pocket picking since no binding site specified

Uploads as dock jobs 32234

Download the pockets picked above together with basic cleanup and normalization of the structure

api.docking.org/v1/dock/32234/download/all

Upload a structure and a binding site specification, but still request that pockets be picked:

api.docking.org/v1/dock/upload/rec=rec.pdb&lig=xtal-lig.pdb&pick=true

Covalent docking. Upload a structure, and scan for eligible covalent attachment points.

api.docking.org/v1/covalent/rec=rec.pdb

covalent docking. Upload a structure and a covalent attachment point.

api.docking.org/v1/covalent/rec=rec.pdb&site=Asp A 234

Covalent docking. Prepare library for covalent docking.

api.docking.org/v1/covalent/library/list1/list2/reactionsmarts

where list1 and list2 is a previously created subset using the zinc api and reaction smarts is a chemical reaction to combine molecule from list1 with molecules from list2 to create a new combinatorial library.

covalent docking. prepare hot covalent docking library.