Interpro Domain Arch Tools

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

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

Available Tools

InterPro_get_clan_members (Type: InterProDomainArchTool)

Get all member families in a Pfam clan (superfamily) using the InterPro API. Pfam clans group rel…

InterPro_get_clan_members tool specification

Tool Information:

  • Name: InterPro_get_clan_members

  • Type: InterProDomainArchTool

  • Description: Get all member families in a Pfam clan (superfamily) using the InterPro API. Pfam clans group related families that share a common evolutionary origin. Returns member family accessions, names, types, and relationship scores. Example: CL0016 (PKinase) contains 30+ member families including PF00069 (Protein kinase), PF03770 (Inositol polyphosphate kinase), PF02958 (EcKL), and many others. Useful for understanding domain superfamily relationships and finding distantly related proteins.

Parameters:

  • clan_accession (string) (required) Pfam clan accession. Examples: ‘CL0016’ (PKinase superfamily, 30+ families), ‘CL0023’ (P53-like transcription factor), ‘CL0004’ (EGF superfamily), ‘CL0159’ (E2 superfamily).

  • max_results (integer) (optional) Maximum number of member families to return (default 50, max 200).

Example Usage:

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

InterPro_get_protein_domain_architecture (Type: InterProDomainArchTool)

Get the complete Pfam domain architecture for a protein with exact residue positions using the In…

InterPro_get_protein_domain_architecture tool specification

Tool Information:

  • Name: InterPro_get_protein_domain_architecture

  • Type: InterProDomainArchTool

  • Description: Get the complete Pfam domain architecture for a protein with exact residue positions using the InterPro API. Returns all Pfam domains mapped to the protein with start/end coordinates, E-values, and integrated InterPro entries. Much more detailed than simple domain lists - includes precise domain boundaries essential for understanding protein function. Example: P04637 (TP53, 393aa) has 4 Pfam domains: PF00870 (P53 DNA-binding, 100-288), PF07710 (tetramerisation, 319-357), PF08563 (transactivation, 6-30), PF18521 (transactivation domain 2, 35-59).

Parameters:

  • accession (string) (required) UniProt protein accession. Examples: ‘P04637’ (TP53, 4 Pfam domains), ‘P00533’ (EGFR), ‘P38398’ (BRCA1), ‘P01308’ (Insulin).

Example Usage:

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

InterPro_get_structures_for_domain (Type: InterProDomainArchTool)

Find all PDB structures containing a specific Pfam domain using the InterPro API. Returns experim…

InterPro_get_structures_for_domain tool specification

Tool Information:

  • Name: InterPro_get_structures_for_domain

  • Type: InterProDomainArchTool

  • Description: Find all PDB structures containing a specific Pfam domain using the InterPro API. Returns experimental structures (X-ray, cryo-EM, NMR) that contain the specified domain, with resolution and experiment type. Useful for finding structural templates for a domain of interest. Example: PF00870 (P53 DNA-binding domain) has 215 PDB structures; PF00069 (Protein kinase) has 5,238 structures. Results sorted by most recent.

Parameters:

  • pfam_accession (string) (required) Pfam domain accession. Examples: ‘PF00870’ (P53 DNA-binding, 215 structures), ‘PF00069’ (Protein kinase, 5238 structures), ‘PF07710’ (P53 tetramerisation), ‘PF00046’ (Homeodomain).

  • max_results (integer) (optional) Maximum number of PDB structures to return (default 20, max 200).

Example Usage:

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