Interpro Member Db Tools

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

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

Available Tools

InterPro_get_member_signature (Type: InterProMemberDBTool)

Retrieve detail for a single InterPro MEMBER-DATABASE signature (not an integrated InterPro IPR e…

InterPro_get_member_signature tool specification

Tool Information:

  • Name: InterPro_get_member_signature

  • Type: InterProMemberDBTool

  • Description: Retrieve detail for a single InterPro MEMBER-DATABASE signature (not an integrated InterPro IPR entry). Member databases include Pfam (PF…), SMART (SM…), PANTHER (PTHR…), CDD (cd…), NCBIfam/TIGRFAM (NF…/TIGR…), SUPERFAMILY (SSF…), CATH-Gene3D (G3DSA…), PRINTS (PR…), HAMAP, PIRSF, PROSITE patterns/profiles, SFLD, and AntiFam. Returns the signature name, type (family/domain/homologous_superfamily/site), the integrated InterPro entry it maps to (if any), description, GO terms, and protein/structure/taxa counts. Distinct from InterPro_get_domain_details which only accepts integrated IPR accessions. No API key.

Parameters:

  • member_database (string) (required) Member database slug: pfam, smart, panther, cdd, ncbifam (TIGRFAM), ssf (SUPERFAMILY), cathgene3d (gene3d), prints, hamap, pirsf, profile (PROSITE profiles), prosite (PROSITE patterns), sfld, antifam. Common aliases (superfamily, gene3d, cath, tigrfam) are accepted.

  • accession (string) (required) The member-database signature accession, e.g. PF00069 (Pfam), SM00002 (SMART), PTHR10000 (PANTHER), NF000004 (NCBIfam), SSF52540 (SUPERFAMILY).

Example Usage:

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

InterPro_get_structures_for_entry (Type: InterProMemberDBTool)

List the experimentally-solved PDB structures whose chains contain a given InterPro domain/family…

InterPro_get_structures_for_entry tool specification

Tool Information:

  • Name: InterPro_get_structures_for_entry

  • Type: InterProMemberDBTool

  • Description: List the experimentally-solved PDB structures whose chains contain a given InterPro domain/family. Returns each PDB structure’s id, title, experiment type (e.g. x-ray, electron microscopy), and resolution, plus the total structure count for that InterPro entry. Useful for finding crystallographic / cryo-EM examples of a domain. Input is an integrated InterPro accession (IPR…). No API key.

Parameters:

  • interpro_id (string) (required) An integrated InterPro accession, e.g. IPR000719 (Protein kinase domain).

  • page_size (integer) (optional) Number of structures to return (1-100, default 20).

Example Usage:

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

InterPro_list_member_databases (Type: InterProMemberDBTool)

List the InterPro member-database catalog with entry counts. Returns the number of signatures con…

InterPro_list_member_databases tool specification

Tool Information:

  • Name: InterPro_list_member_databases

  • Type: InterProMemberDBTool

  • Description: List the InterPro member-database catalog with entry counts. Returns the number of signatures contributed by each member database (Pfam, CATH-Gene3D, SUPERFAMILY/ssf, PANTHER, CDD, PROSITE profiles/patterns, SMART, NCBIfam, PRINTS, HAMAP, PIRSF, SFLD, AntiFam) plus the integrated, unintegrated, InterPro and overall totals. Useful as a discovery/overview call before browsing a specific member database. No API key, no parameters.

Parameters:

No parameters required.

Example Usage:

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

InterPro_list_member_signatures (Type: InterProMemberDBTool)

Browse / paginate the signature catalog of a single InterPro member database. Returns a page of m…

InterPro_list_member_signatures tool specification

Tool Information:

  • Name: InterPro_list_member_signatures

  • Type: InterProMemberDBTool

  • Description: Browse / paginate the signature catalog of a single InterPro member database. Returns a page of member-database signatures (accession, name, type, and the integrated InterPro entry each maps to) plus the total count for that database. Useful for surveying what a member database (Pfam, SMART, PANTHER, CDD, NCBIfam, SUPERFAMILY, CATH-Gene3D, PRINTS, HAMAP, PIRSF, PROSITE, SFLD, AntiFam) contains. Optionally filter by entry type (family, domain, homologous_superfamily, site). No API key.

Parameters:

  • member_database (string) (required) Member database slug: pfam, smart, panther, cdd, ncbifam, ssf, cathgene3d, prints, hamap, pirsf, profile, prosite, sfld, antifam. Aliases (superfamily, gene3d, tigrfam) accepted.

  • entry_type (string) (optional) Optional filter by entry type: family, domain, homologous_superfamily, or site.

  • page_size (integer) (optional) Number of signatures to return per page (1-100, default 20).

Example Usage:

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