Ebi Proteins Features Tools

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

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

Available Tools

EBIProteins_get_domains_sites (Type: EBIProteinsFeaturesTool)

Get domain and site features for a protein from the EBI Proteins API. Returns binding sites, DNA-…

EBIProteins_get_domains_sites tool specification

Tool Information:

  • Name: EBIProteins_get_domains_sites

  • Type: EBIProteinsFeaturesTool

  • Description: Get domain and site features for a protein from the EBI Proteins API. Returns binding sites, DNA-binding regions, active sites, motifs, regions of interest, and zinc finger domains annotated in UniProtKB. Complements InterPro domain annotations by providing more granular functional site information. Example: P04637 (TP53) returns 31 features including DNA-binding domain (residues 102-292), interaction regions with MDM2/CCAR2/HRMT1L2, zinc binding sites, and p53 transactivation motifs.

Parameters:

  • accession (string) (required) UniProt accession. Examples: ‘P04637’ (TP53/p53), ‘P00533’ (EGFR), ‘P01308’ (Insulin), ‘P31749’ (AKT1).

Example Usage:

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

EBIProteins_get_molecule_processing (Type: EBIProteinsFeaturesTool)

Get molecule processing features for a protein from the EBI Proteins API. Returns signal peptides…

EBIProteins_get_molecule_processing tool specification

Tool Information:

  • Name: EBIProteins_get_molecule_processing

  • Type: EBIProteinsFeaturesTool

  • Description: Get molecule processing features for a protein from the EBI Proteins API. Returns signal peptides, transit peptides, mature protein chains, propeptides, and initiator methionine annotations. Essential for understanding how a protein precursor is processed into its functional form. Example: P01308 (Insulin) returns signal peptide (1-24), B chain (25-54), C peptide (57-87), and A chain (90-110) showing the complete insulin processing pathway.

Parameters:

  • accession (string) (required) UniProt accession. Examples: ‘P01308’ (Insulin - classic example), ‘P01375’ (TNF-alpha), ‘P01189’ (POMC - multiple peptides), ‘P06213’ (Insulin receptor).

Example Usage:

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

EBIProteins_get_structural_features (Type: EBIProteinsFeaturesTool)

Get secondary structure annotations for a protein from the EBI Proteins API. Returns helix, beta …

EBIProteins_get_structural_features tool specification

Tool Information:

  • Name: EBIProteins_get_structural_features

  • Type: EBIProteinsFeaturesTool

  • Description: Get secondary structure annotations for a protein from the EBI Proteins API. Returns helix, beta strand, and turn assignments mapped to the UniProt protein sequence. These are derived from experimental 3D structures and mapped to the canonical sequence, providing a comprehensive secondary structure profile. Example: P04637 (TP53) returns 40 structural features including helices (residues 19-29, 165-172, etc.), strands (residues 112-114, 141-143, etc.), and turns.

Parameters:

  • accession (string) (required) UniProt accession. Examples: ‘P04637’ (TP53/p53), ‘P69905’ (Hemoglobin alpha), ‘P00533’ (EGFR), ‘P38398’ (BRCA1).

Example Usage:

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