Elm Tools#

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

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

Available Tools#

ELM_get_instances (Type: ELMTool)#

Get experimentally validated short linear motif (SLiM) instances for a protein from the ELM datab…

ELM_get_instances tool specification

Tool Information:

  • Name: ELM_get_instances

  • Type: ELMTool

  • Description: Get experimentally validated short linear motif (SLiM) instances for a protein from the ELM database. Returns motif positions, types (CLV=cleavage, DEG=degradation/degrons, DOC=docking, LIG=ligand binding, MOD=modification sites, TRG=targeting signals), experimental methods used for validation, PubMed references, and PDB structures where the motif was observed. SLiMs are compact protein interaction interfaces (3-11 residues) that mediate regulatory functions. Use with UniProt accession (e.g., P04637 for TP53).

Parameters:

  • operation (string) (optional) Operation type

  • uniprot_id ([‘string’, ‘null’]) (optional) UniProt accession, e.g., P04637 (TP53), P00533 (EGFR), P38398 (BRCA1), P42336 (PIK3CA)

  • uniprot_acc ([‘string’, ‘null’]) (optional) Alias for uniprot_id. UniProt accession, e.g., P04637 (TP53)

  • motif_type ([‘string’, ‘null’]) (optional) Filter by motif functional type. CLV=cleavage sites, DEG=degradation motifs, DOC=docking sites, LIG=ligand binding, MOD=modification sites, TRG=targeting signals. Omit for all types.

Example Usage:

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

ELM_get_interaction_domains (Type: ELMTool)#

Get ELM motif-to-interaction-domain mappings with exact total and recoverable offset pagination. …

ELM_get_interaction_domains tool specification

Tool Information:

  • Name: ELM_get_interaction_domains

  • Type: ELMTool

  • Description: Get ELM motif-to-interaction-domain mappings with exact total and recoverable offset pagination. Continue with metadata.next_offset while metadata.has_more is true. Filters are applied before pagination.

Parameters:

  • operation (string) (optional) Operation type

  • elm_identifier ([‘string’, ‘null’]) (optional) Filter to a single ELM class identifier (e.g., ‘CLV_NRD_NRD_1’, ‘LIG_SH3_1’). Omit to return all mappings.

  • query ([‘string’, ‘null’]) (optional) Free-text filter matched against ELM identifier, Pfam accession, domain name, and description (e.g., ‘WD40’, ‘PF00082’, ‘kinase’, ‘SH3’).

  • max_results (integer) (optional) Maximum mappings to return (default: 100, max: 500 covers all 427 mappings)

  • offset (integer) (optional) Zero-based offset in the filtered mapping list.

Example Usage:

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

ELM_list_classes (Type: ELMTool)#

List ELM short linear motif classes with exact total and recoverable offset pagination. Continue …

ELM_list_classes tool specification

Tool Information:

  • Name: ELM_list_classes

  • Type: ELMTool

  • Description: List ELM short linear motif classes with exact total and recoverable offset pagination. Continue with metadata.next_offset while metadata.has_more is true. Filters are applied before pagination.

Parameters:

  • operation (string) (optional) Operation type

  • motif_type ([‘string’, ‘null’]) (optional) Filter by motif functional type. CLV=cleavage, DEG=degradation, DOC=docking, LIG=ligand binding, MOD=modification, TRG=targeting. Omit for all types.

  • query ([‘string’, ‘null’]) (optional) Search keyword to filter by name, identifier, or description. E.g., ‘caspase’, ‘kinase’, ‘ubiquitin’, ‘nuclear’

  • max_results (integer) (optional) Maximum results to return (default: 50, max: 400 covers all classes)

  • offset (integer) (optional) Zero-based offset in the filtered motif-class list.

Example Usage:

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