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) (required) 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": {
        "operation": "example_value"
    }
}
result = tu.run(query)

ELM_get_interaction_domains (Type: ELMTool)

Get the ELM motif-to-interaction-domain mapping: for each Short Linear Motif (SLiM) class, the pr…

ELM_get_interaction_domains tool specification

Tool Information:

  • Name: ELM_get_interaction_domains

  • Type: ELMTool

  • Description: Get the ELM motif-to-interaction-domain mapping: for each Short Linear Motif (SLiM) class, the protein domain (with Pfam accession) that recognizes/binds the motif. SLiMs (3-11 residue motifs) are bound by globular domains on partner proteins; this mapping links each ELM class to the Pfam domain family of its binding partner, enabling reconstruction of the domain-motif interaction network. Returns ~409 motif-to-domain mapping records across all ELM classes. Filter by a specific elm_identifier or a free-text query (Pfam accession, domain name/description). Example: CLV_NRD_NRD_1 -> PF00675 ‘Peptidase_M16’ (Insulinase); CLV_PCSK_FUR_1 -> PF00082 ‘Peptidase_S8’ (Subtilase family); DEG_APCC_DBOX_1 -> PF00400 ‘WD40’.

Parameters:

  • operation (string) (required) 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)

Example Usage:

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

ELM_list_classes (Type: ELMTool)

List short linear motif (SLiM) classes from the ELM database. Each class represents a distinct ty…

ELM_list_classes tool specification

Tool Information:

  • Name: ELM_list_classes

  • Type: ELMTool

  • Description: List short linear motif (SLiM) classes from the ELM database. Each class represents a distinct type of functional motif with a regex pattern, description, and statistics on known instances. Filter by functional type (CLV/DEG/DOC/LIG/MOD/TRG) or search by keyword (e.g., ‘caspase’, ‘phosphorylation’, ‘nuclear’, ‘ubiquitin’). The regex patterns can be used to scan protein sequences for potential motif matches. ELM contains 353 motif classes covering cleavage, degradation, docking, ligand binding, modification, and targeting functions.

Parameters:

  • operation (string) (required) 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)

Example Usage:

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