BindingDB logo
myBDB logout
BindingDB RESTful API

BindingDB Web Services


RESTful API

The following lists the BindingDB RESTful API. The returned results are in the XML format.

getLigandsByUniprots:

http://bindingdb.org/axis2/services/BDBService/getLigandsByUniprots?uniprot={UNIPROTid1,id2,...}&cutoff={1000}&code=[012]&response=application/json

This service returns all binding data for protein target(s) identified by UniProt identifier(s), within some user-specified affinity cutoff. One may also optionally request data for only compounds we have identified as commercially available, or compounds we have identified as being FDA-approved drugs. The output is provided in XML format by default, but JSON format is provided if requested in the input query. If there is no matching UNIPROT ID in BindingDB, the result is an empty string.

Request Type:
GET

Parameters:
String - uniprot (UNIPROT identifiers separated by commas)
Number - coutoff (affinity cutoff value, in nM)
Number [012] - code (0 returns results for any BindingDB compound; 1 returns results for only commercially available compounds; 2 returns results for only FDA approved compounds)
String - response (allows specification of JSON format default is XML)

Output:
A list of monomerIDs with associated SMILES strings, affinity types, and affinity values

Example:
To get the BindingDB measurements for UNIPROT targets P35355 and Q8HZR1, with affinity cutoff 1000nM, across all BindingDB compounds, with results in JSON use:
http://www.bindingdb.org/axis2/services/BDBService/getLigandsByUniprots?uniprot=P35355,Q8HZR1&cutoff=1000&code=0&response=application/json
Note that omitting "&response=application/json" will give XML output.
For best performance, and to protect the BindingDB servers, please separate consecutive requests for this service by a time interval of at least 1 second.

getLigandsByUniprot:

http://bindingdb.org/axis2/services/BDBService/getLigandsByUniprot?uniprot={UNIPROT};{IC50cutoff}

This service is designed to return all binding data for a protein, within some affinity cutoff. The user passes a UNIPROT database identifier, along with optional affinity cutoff, and receives BindingDB results in XML. If there is no matching UNIPROT ID in the database, it will return an empty string.

Request Type:
GET

Parameters:
String - UNIPROT
Integer - affinity cutoff value

Output:
A list of monomerIDs with associated SMILES strings, affinity types, and affinity values

Example:
To get the BindingDB measurements for UNIPROT target P35355 at affinity cutoff IC50=100, use:
http://bindingdb.org/axis2/services/BDBService/getLigandsByUniprot?uniprot=P35355;100

getTargetByCompound:

http://bindingdb.org/axis2/services/BDBService/getTargetByCompound?smiles={SMILES}&cutoff={similarity_cutoff}

This service provides the ability to retrieve binding data for a particular small molecule compound. Specifically, a user-described compound is screened for other compounds in BindingDB of similar structure (within a given similarity cutoff) and this list of similar compounds is returned. For each of these compounds, binding targets and associated affinities are also included. To use, the user simply passes a compound structure in SMILES format, along with optional similarity cutoff, and receives the BindingDB results in XML. If there is no matching compound structure in the database, it will return an empty string.

Request Type:
GET

Parameters:
String - SMILES
Decimal - similarity cutoff value

Output:
List of similar compounds along with their protein targets, including associated affinity types and measurements

Example:
To get the measurements for a compound converted to SMILES, use:
http://bindingdb.org/axis2/services/BDBService/getTargetByCompound?smiles=CCC[Ni%2B]%28C%29%28C%29CCn1nncc1COc1cc%28=O%29n%28C%29c2ccccc12&cutoff=0.85