Bindingdb Tools#

Configuration File: bindingdb_tools.json Tool Type: Local Tools Count: 5

This page contains all tools defined in the bindingdb_tools.json configuration file.

Available Tools#

BindingDB_get_ligands_by_pdb (Type: BindingDBTool)#

Get binding affinity data for proteins by PDB structure ID. Returns ligands with measured affinit…

BindingDB_get_ligands_by_pdb tool specification

Tool Information:

  • Name: BindingDB_get_ligands_by_pdb

  • Type: BindingDBTool

  • Description: Get binding affinity data for proteins by PDB structure ID. Returns ligands with measured affinities for the protein structure. Useful for structure-activity relationship analysis when you have co-crystal structures.

Parameters:

  • pdb_ids (string) (required) Comma-separated PDB IDs (e.g., 1Q0L,3ANM)

  • affinity_cutoff (integer) (optional) Maximum affinity in nM (default: 10000)

  • sequence_identity (integer) (optional) Minimum sequence identity % (default: 100)

Example Usage:

query = {
    "name": "BindingDB_get_ligands_by_pdb",
    "arguments": {
        "pdb_ids": "example_value"
    }
}
result = tu.run(query)

BindingDB_get_ligands_by_uniprot (Type: BindingDBTool)#

Get binding affinity data (Ki, IC50, Kd) for a single protein by UniProt ID. Returns SMILES struc…

BindingDB_get_ligands_by_uniprot tool specification

Tool Information:

  • Name: BindingDB_get_ligands_by_uniprot

  • Type: BindingDBTool

  • Description: Get binding affinity data (Ki, IC50, Kd) for a single protein by UniProt ID. Returns SMILES structures and measured affinities from BindingDB. Essential for drug discovery target analysis. Example: P00533 (EGFR) returns known inhibitors with binding constants.

Parameters:

  • affinity_cutoff (integer) (optional) Maximum affinity in nM (default: 10000)

  • uniprot_id (string) (required) UniProt accession ID (e.g., P00533 for EGFR)

Example Usage:

query = {
    "name": "BindingDB_get_ligands_by_uniprot",
    "arguments": {
        "uniprot_id": "example_value"
    }
}
result = tu.run(query)

BindingDB_get_ligands_by_uniprots (Type: BindingDBTool)#

Get binding affinity data for multiple proteins by UniProt IDs. Returns SMILES and affinities for…

BindingDB_get_ligands_by_uniprots tool specification

Tool Information:

  • Name: BindingDB_get_ligands_by_uniprots

  • Type: BindingDBTool

  • Description: Get binding affinity data for multiple proteins by UniProt IDs. Returns SMILES and affinities for all matching ligands. Use for comparing binding profiles across protein family members or paralogs.

Parameters:

  • affinity_cutoff (integer) (optional) Maximum affinity in nM (default: 10000)

  • uniprot_ids (string) (required) Comma-separated UniProt IDs (e.g., P00176,P00183)

Example Usage:

query = {
    "name": "BindingDB_get_ligands_by_uniprots",
    "arguments": {
        "uniprot_ids": "example_value"
    }
}
result = tu.run(query)

BindingDB_get_targets_by_compound (Type: BindingDBTool)#

Find protein targets for a compound by SMILES (Simplified Molecular Input Line Entry System) stru…

BindingDB_get_targets_by_compound tool specification

Tool Information:

  • Name: BindingDB_get_targets_by_compound

  • Type: BindingDBTool

  • Description: Find protein targets for a compound by SMILES (Simplified Molecular Input Line Entry System) structure. Returns proteins with binding affinity data for compounds BindingDB considers similar; the breadth of that similarity set is fixed by BindingDB and is not caller-adjustable. Essential for polypharmacology analysis and off-target prediction.

Parameters:

  • smiles (string) (required) SMILES structure of compound

  • similarity_cutoff (number) (optional) NOT APPLIED: BindingDB’s getTargetByCompound endpoint ignores this threshold - every value tested from 0.4 to 1.0, and omitting it entirely, returns the identical result set (verified against four chemically diverse compounds). The value is accepted and forwarded for forward compatibility and echoed back as ‘similarity’ in the response, so do not rely on it to narrow results; filter the returned affinities yourself if you need a tighter match.

Example Usage:

query = {
    "name": "BindingDB_get_targets_by_compound",
    "arguments": {
        "smiles": "example_value"
    }
}
result = tu.run(query)

BindingDB_search_by_target (Type: BindingDBTool)#

Search BindingDB for binding affinity data by target. Requires a UniProt accession (e.g. ‘P00533’…

BindingDB_search_by_target tool specification

Tool Information:

  • Name: BindingDB_search_by_target

  • Type: BindingDBTool

  • Description: Search BindingDB for binding affinity data by target. Requires a UniProt accession (e.g. ‘P00533’); free-text gene or protein names are not supported by BindingDB’s REST API — use ChEMBL_search_target or PubChem BioAssay for name-based lookup. To query by UniProt ID directly, BindingDB_get_ligands_by_uniprot is equivalent.

Parameters:

  • query (string) (required) Target gene symbol or protein name (e.g., ‘EGFR’, ‘BRAF’, ‘kinase’)

  • target (string) (optional) Alias for query. Target gene symbol or protein name.

Example Usage:

query = {
    "name": "BindingDB_search_by_target",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)