Iptmnet Tools

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

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

Available Tools

iPTMnet_get_proteoforms (Type: iPTMnetTool)

Get proteoform records for a protein from iPTMnet. Proteoforms represent specific combinations of…

iPTMnet_get_proteoforms tool specification

Tool Information:

  • Name: iPTMnet_get_proteoforms

  • Type: iPTMnetTool

  • Description: Get proteoform records for a protein from iPTMnet. Proteoforms represent specific combinations of PTM sites on a protein, as defined by the PRO ontology. Each proteoform has a PRO ID, modified sites, the responsible enzyme (if known), source database, and PubMed references. Useful for understanding which specific PTM combinations have been experimentally observed. Use with UniProt accession (e.g., P04637 for TP53).

Parameters:

  • operation (string) (required) Operation type

  • uniprot_id (string) (required) UniProt accession, e.g., P04637 (TP53), P00533 (EGFR), P31749 (AKT1)

Example Usage:

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

iPTMnet_get_ptm_ppi (Type: iPTMnetTool)

Get PTM-dependent protein-protein interactions from iPTMnet. Returns interactions where a post-tr…

iPTMnet_get_ptm_ppi tool specification

Tool Information:

  • Name: iPTMnet_get_ptm_ppi

  • Type: iPTMnetTool

  • Description: Get PTM-dependent protein-protein interactions from iPTMnet. Returns interactions where a post-translational modification on one protein affects its binding to another protein. Each interaction includes the PTM type, modified substrate with site position, the interacting partner, association type (association/dissociation), data source, and PubMed reference. Essential for understanding how PTMs regulate protein interaction networks. Use with UniProt accession (e.g., P04637 for TP53).

Parameters:

  • operation (string) (required) Operation type

  • uniprot_id (string) (required) UniProt accession, e.g., P04637 (TP53), P00533 (EGFR), P31749 (AKT1)

  • ptm_type ([‘string’, ‘null’]) (optional) Filter by PTM type: Phosphorylation, Acetylation, Ubiquitination, Methylation. Case-insensitive. Omit to return all types.

Example Usage:

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

iPTMnet_get_ptm_sites (Type: iPTMnetTool)

Get all post-translational modification (PTM) sites for a protein from iPTMnet. Returns residue, …

iPTMnet_get_ptm_sites tool specification

Tool Information:

  • Name: iPTMnet_get_ptm_sites

  • Type: iPTMnetTool

  • Description: Get all post-translational modification (PTM) sites for a protein from iPTMnet. Returns residue, position, PTM type, confidence score, source databases, catalytic enzymes, and PubMed references for each site. Data aggregated from PhosphoSitePlus, UniProt, and text mining. Covers phosphorylation, acetylation, ubiquitination, methylation, glycosylation, sumoylation, and more. Results organized by protein isoform. Use with UniProt accession (e.g., P04637 for TP53).

Parameters:

  • operation (string) (required) Operation type

  • uniprot_id (string) (required) UniProt accession, e.g., P04637 (TP53), P00533 (EGFR), P31749 (AKT1), Q16539 (MAPK14/p38)

  • ptm_type ([‘string’, ‘null’]) (optional) Filter by PTM type: Phosphorylation, Acetylation, Ubiquitination, Methylation, Sumoylation, N-Glycosylation, O-Glycosylation, S-Nitrosylation. Case-insensitive. Omit to return all types.

Example Usage:

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

iPTMnet_search (Type: iPTMnetTool)

Search the iPTMnet database for proteins with post-translational modification (PTM) data. Find pr…

iPTMnet_search tool specification

Tool Information:

  • Name: iPTMnet_search

  • Type: iPTMnetTool

  • Description: Search the iPTMnet database for proteins with post-translational modification (PTM) data. Find proteins by gene name, protein name, or keyword. Filter by role (Substrate = modified protein, Enzyme = modifier) and PTM type (Phosphorylation, Acetylation, Ubiquitination, Methylation, etc.). iPTMnet integrates data from PhosphoSitePlus, UniProt, PRO ontology, and text mining. Returns UniProt IDs, PTM site counts, enzyme/substrate roles, and isoform counts.

Parameters:

  • operation (string) (optional) Operation type

  • search_term (string) (optional) Search query: gene name (TP53, EGFR, AKT1), protein name (p53, insulin receptor), or keyword (kinase, ubiquitin)

  • role (string) (optional) Filter by protein role. Substrate = proteins that are modified; Enzyme = proteins that modify others. Default: Substrate

  • ptm_type ([‘string’, ‘null’]) (optional) Filter by PTM type: Phosphorylation, Acetylation, Ubiquitination, Methylation, Sumoylation, N-Glycosylation, O-Glycosylation, S-Nitrosylation, etc. Case-sensitive. Omit to return all types.

  • term_type (string) (optional) Type of search term. Default: All (searches across all fields)

  • max_results (integer) (optional) Maximum results to return (default: 25)

  • query (string) (optional) Gene name, protein name, or keyword to search (alias for search_term)

Example Usage:

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