Bindingdb Tools

Configuration File: bindingdb_tools.json Tool Type: Local Tools Count: 4

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:

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

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

Example Usage:

query = {
    "name": "BindingDB_get_ligands_by_uniprot",
    "arguments": {
        "uniprot": "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:

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

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

Example Usage:

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

BindingDB_get_targets_by_compound (Type: BindingDBTool)

Find protein targets for a compound by SMILES structure. Returns proteins with binding affinity d…

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 structure. Returns proteins with binding affinity data for similar compounds. Essential for polypharmacology analysis and off-target prediction.

Parameters:

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

  • similarity_cutoff (number) (optional) Similarity threshold 0-1 (default: 0.85)

Example Usage:

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