Alphafold Tools

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

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

Available Tools

alphafold_get_annotations (Type: AlphaFoldRESTTool)

Retrieve AlphaFold variant annotations (e.g., missense mutations) for a given UniProt accession (…

alphafold_get_annotations tool specification

Tool Information:

  • Name: alphafold_get_annotations

  • Type: AlphaFoldRESTTool

  • Description: Retrieve AlphaFold variant annotations (e.g., missense mutations) for a given UniProt accession (e.g., ‘P69905’). Input must be a UniProt accession, entry name, or CRC64 checksum, along with an annotation type (currently only ‘MUTAGEN’). Use this tool to explore predicted pathogenicity or functional effects of substitutions. If you only have a protein/gene name, resolve it with uniprot_search. For experimentally curated variants, use UniProt_get_disease_variants_by_accession. To view the full 3D structure, call alphafold_get_prediction; for overall model metadata, use alphafold_get_summary.

Parameters:

  • qualifier (string) (required) Protein identifier: UniProt accession, entry name, or CRC64 checksum.

  • type (string) (required) Annotation type (currently only ‘MUTAGEN’ is supported).

Example Usage:

query = {
    "name": "alphafold_get_annotations",
    "arguments": {
        "qualifier": "example_value",
        "type": "example_value"
    }
}
result = tu.run(query)

alphafold_get_prediction (Type: AlphaFoldRESTTool)

Retrieve full AlphaFold 3D structure predictions for a given protein. Input must be a UniProt acc…

alphafold_get_prediction tool specification

Tool Information:

  • Name: alphafold_get_prediction

  • Type: AlphaFoldRESTTool

  • Description: Retrieve full AlphaFold 3D structure predictions for a given protein. Input must be a UniProt accession (e.g., ‘P69905’), UniProt entry name (e.g., ‘HBA_HUMAN’), or CRC64 checksum. Returns residue-level metadata including sequence, per-residue confidence scores (pLDDT), and structure download links (PDB, CIF, PAE). If you do not know the accession, first call uniprot_search to resolve it from a protein/gene name, or UniProt_get_entry_by_accession if you already have the accession and want UniProt details. For a quick overview, use alphafold_get_summary. For mutation/variant impact, see `alphafold_get_annotations.

Parameters:

  • qualifier (string) (required) Protein identifier: UniProt accession (e.g., ‘P69905’), entry name (e.g., ‘HBA_HUMAN’), or CRC64 checksum.

  • sequence_checksum (string) (optional) Optional CRC64 checksum of the UniProt sequence.

Example Usage:

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

alphafold_get_summary (Type: AlphaFoldRESTTool)

Retrieve summary details of AlphaFold 3D models for a given protein. Input must be a UniProt acce…

alphafold_get_summary tool specification

Tool Information:

  • Name: alphafold_get_summary

  • Type: AlphaFoldRESTTool

  • Description: Retrieve summary details of AlphaFold 3D models for a given protein. Input must be a UniProt accession, entry name, or CRC64 checksum. Returns lightweight information such as sequence length, coverage, confidence scores, experimental method, resolution, oligomeric state, and structural entities. If you only know the protein/gene name, first use uniprot_search to find the accession. For full residue-level 3D predictions with downloadable coordinates, call alphafold_get_prediction. For curated variants, see UniProt_get_disease_variants_by_accession; for predicted mutation effects, use alphafold_get_annotations.

Parameters:

  • qualifier (string) (required) Protein identifier: UniProt accession, entry name, or CRC64 checksum.

Example Usage:

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