Alphamissense Tools

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

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

Available Tools

AlphaMissense_get_protein_scores (Type: AlphaMissenseTool)

Get AlphaMissense pathogenicity scores for EVERY residue of a protein in one call. The upstream h…

AlphaMissense_get_protein_scores tool specification

Tool Information:

  • Name: AlphaMissense_get_protein_scores

  • Type: AlphaMissenseTool

  • Description: Get AlphaMissense pathogenicity scores for EVERY residue of a protein in one call. The upstream hegelab API only exposes per-residue queries; this tool hides that by looking up the protein length from UniProt and concurrently fetching all residues via a thread pool. Returns a list of per-position records (one per residue) plus protein length, count of successful fetches, and the pathogenic/ambiguous/benign thresholds. Use this when you want whole-protein vulnerability assessment, hotspot detection, or to build a (20 × n_positions) AlphaMissense score matrix for benchmarking. Set max_residues > 0 to cap the loop for fast diagnostic calls.

Parameters:

  • uniprot_id (string) (required) UniProt accession ID (e.g., ‘P00533’ for EGFR, ‘P01116’ for KRAS, ‘P04637’ for TP53).

  • max_residues ([‘integer’, ‘null’]) (optional) Optional cap on the number of residues fetched. 0 / null / omitted = no cap (fetch every residue of the protein, recommended for whole-protein analysis). Positive integer = fetch only the first N residues (useful for fast diagnostic calls on very long proteins).

Example Usage:

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

AlphaMissense_get_residue_scores (Type: AlphaMissenseTool)

Get AlphaMissense scores for all 20 possible amino acid substitutions at a specific protein posit…

AlphaMissense_get_residue_scores tool specification

Tool Information:

  • Name: AlphaMissense_get_residue_scores

  • Type: AlphaMissenseTool

  • Description: Get AlphaMissense scores for all 20 possible amino acid substitutions at a specific protein position. Useful for saturation mutagenesis analysis and identifying pathogenic hotspots.

Parameters:

  • uniprot_id (string) (required) UniProt accession ID (e.g., ‘P00533’ for EGFR)

  • position (integer) (required) Amino acid position in the protein (1-indexed)

Example Usage:

query = {
    "name": "AlphaMissense_get_residue_scores",
    "arguments": {
        "uniprot_id": "example_value",
        "position": 10
    }
}
result = tu.run(query)

AlphaMissense_get_variant_score (Type: AlphaMissenseTool)

Get AlphaMissense pathogenicity score for a specific missense variant. Input: UniProt ID and vari…

AlphaMissense_get_variant_score tool specification

Tool Information:

  • Name: AlphaMissense_get_variant_score

  • Type: AlphaMissenseTool

  • Description: Get AlphaMissense pathogenicity score for a specific missense variant. Input: UniProt ID and variant (e.g., ‘p.R123H’). Returns score and classification (pathogenic/ambiguous/benign). State-of-the-art for VUS interpretation.

Parameters:

  • uniprot_id (string) (required) UniProt accession ID (e.g., ‘P00533’ for EGFR)

  • variant (string) (required) Variant in protein notation: p.X123Y or X123Y where X is reference amino acid, 123 is position, Y is variant (e.g., ‘p.R123H’, ‘V600E’)

Example Usage:

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