We offer an application programming interface to carry out complex queries. In general, queries are asynchronous. That is:
- make a request
- retrieve the results
This is the 2015 version of this service. To get a list of services offered, please browse to [api15.docking.org api15.docking.org]. Requests may be invoked starting from a web page, or by using curl or wget. As much as possible, each operation is atomic, that is, you make the request and get the response, and that is the end of it. We plan to support a hand-off model in which the results of one request may be used by a following request without downloading the files to your client computer.
Docking remains too difficult for many people, even experts. One of the reasons is that it requires a complex software and hardware environment that requires much effort and ongoing maintenance. The purpose of this API is to make important steps in the docking process more accessible. The major application areas are:
- docking - non covalent docking
- covalent - covalent docking
- zinc - database preparation and processing, including covalent docking libraries
- decoys - decoys as sanity checks, when actives are available
- action - other cheminformatics operations such as clustering
This API aims to allow all simple transactions to be run under program control on our servers. The user may then elect to download the materials (docking prep files, databases) for local fine tuning on the user's machines, or to continue the calculation with less control on our servers.
- currently no services are available.
Services planned for 2015
- build library for docking - non-covalent
- build library for docking - covalent
- prepare receptor for docking - non-covalent
- prepare receptor for docking - covalent
- run docking controls - non-covalent
- run docking controls - covalent
- dock a library - non-covalent
- dock a library - covalent
- tanimoto lower triangular
- chemical clustering
Service planned for 2016
The URL takes one of two forms
where application is one of: docking, covalent, zinc, decoys, or action, and action and arguments are defined in the relevant section of this page.
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
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
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
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
This is created as job # 556677
Download the docking results for docking on the client
Download the arylsulfonamide database created above in db2 format
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
Upload a structure and a binding site specification, but still request that pockets be picked:
Covalent docking. Upload a structure, and scan for eligible covalent attachment points.
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.
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.