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 all AlphaMissense pathogenicity scores for a protein by UniProt ID. Returns comprehensive res…

AlphaMissense_get_protein_scores tool specification

Tool Information:

  • Name: AlphaMissense_get_protein_scores

  • Type: AlphaMissenseTool

  • Description: Get all AlphaMissense pathogenicity scores for a protein by UniProt ID. Returns comprehensive residue-level data for all possible missense variants across the entire protein. Useful for identifying pathogenic hotspots and overall protein vulnerability assessment.

Parameters:

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

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)