Protacdb Tools

Configuration File: protacdb_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

ProtacDB_get_protac (Type: ProtacDBTool)

Get detailed information about a specific PROTAC compound by its PROTAC-DB ID. Returns full recor…

ProtacDB_get_protac tool specification

Tool Information:

  • Name: ProtacDB_get_protac

  • Type: ProtacDBTool

  • Description: Get detailed information about a specific PROTAC compound by its PROTAC-DB ID. Returns full record including SMILES structure, warhead canonical SMILES, linker, E3 ligand, target protein, DC50 values, Dmax, cell lines tested, and literature references (DOI, journal).

Parameters:

  • operation (string) (required) Operation type

  • protac_id (string) (required) PROTAC-DB compound ID (e.g., ‘1’, ‘42’, ‘100’)

Example Usage:

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

ProtacDB_search_protacs (Type: ProtacDBTool)

Search PROTAC-DB 3.0 for PROTAC (Proteolysis Targeting Chimera) compounds. Filter by target prote…

ProtacDB_search_protacs tool specification

Tool Information:

  • Name: ProtacDB_search_protacs

  • Type: ProtacDBTool

  • Description: Search PROTAC-DB 3.0 for PROTAC (Proteolysis Targeting Chimera) compounds. Filter by target protein and/or E3 ligase. Returns PROTAC structures with DC50, Dmax, SMILES, cell line, and pharmacological data. At least one of target or e3_ligase is required. Use for: finding PROTACs targeting BRD4, KRAS, AR; comparing CRBN vs VHL-based PROTACs.

Parameters:

  • operation (string) (required) Operation type

  • target ([‘string’, ‘null’]) (optional) Target protein name or gene symbol (e.g., ‘BRD4’, ‘KRAS’, ‘AR’, ‘BCL2’). At least one of target or e3_ligase required.

  • e3_ligase ([‘string’, ‘null’]) (optional) E3 ubiquitin ligase (e.g., ‘CRBN’, ‘VHL’, ‘MDM2’, ‘XIAP’). At least one of target or e3_ligase required.

  • max_results (integer) (optional) Maximum number of compounds to return (default 50, max 100)

Example Usage:

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

ProtacDB_search_targets (Type: ProtacDBTool)

Search PROTAC target proteins in PROTAC-DB 3.0. Returns target protein names (short and long). Ov…

ProtacDB_search_targets tool specification

Tool Information:

  • Name: ProtacDB_search_targets

  • Type: ProtacDBTool

  • Description: Search PROTAC target proteins in PROTAC-DB 3.0. Returns target protein names (short and long). Over 446 unique targets available. Use for: discovering what proteins can be targeted by PROTACs, finding targets by gene symbol or protein name.

Parameters:

  • operation (string) (required) Operation type

  • target_name ([‘string’, ‘null’]) (optional) Target protein name or gene symbol (e.g., ‘BRD4’, ‘KRAS’). Returns all targets if omitted.

  • uniprot_id ([‘string’, ‘null’]) (optional) UniProt accession ID (e.g., ‘O60885’ for BRD4). Mutually exclusive with target_name.

Example Usage:

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