BindingDB Web Services

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RESTful API

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

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