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 MUTAGEN annotations for a given UniProt accession. Returns experimental mutage…

alphafold_get_annotations tool specification

Tool Information:

  • Name: alphafold_get_annotations

  • Type: AlphaFoldRESTTool

  • Description: Retrieve AlphaFold MUTAGEN annotations for a given UniProt accession. Returns experimental mutagenesis data mapped onto protein structures from UniProt. The qualifier must be a UniProt ACCESSION (e.g., ‘P69905’). Note: Not all proteins have MUTAGEN annotations available in the database.

Parameters:

  • qualifier (string) (required) UniProt ACCESSION (e.g., ‘P69905’). Must be an accession number, not an entry name.

Example Usage:

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

alphafold_get_prediction (Type: AlphaFoldRESTTool)

Retrieve full AlphaFold 3D structure predictions for a given protein. IMPORTANT: The qualifier mu…

alphafold_get_prediction tool specification

Tool Information:

  • Name: alphafold_get_prediction

  • Type: AlphaFoldRESTTool

  • Description: Retrieve full AlphaFold 3D structure predictions for a given protein. IMPORTANT: The qualifier must be a UniProt ACCESSION (e.g., ‘P69905’ for HBA_HUMAN). Do NOT use UniProt entry names like ‘HBA_HUMAN’ - they will cause API errors. To find UniProt accession from a gene/protein name, use UniProt_search (e.g., query=’gene:HBA’ organism=’human’) or UniProt_id_mapping for ID conversion. Returns residue-level metadata including sequence, per-residue confidence scores (pLDDT), and structure download links (PDB, CIF, PAE). If you already have the accession and want UniProt details, call UniProt_get_entry_by_accession. 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’). Do NOT use entry names like ‘HBA_HUMAN’. To find accession from gene name: use UniProt_search or UniProt_id_mapping.

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

Example Usage:

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

alphafold_get_summary (Type: AlphaFoldRESTTool)

Retrieve summary details of AlphaFold 3D models for a given protein. IMPORTANT: The qualifier mus…

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. IMPORTANT: The qualifier must be a UniProt ACCESSION (e.g., ‘Q5SWX9’ for MEIOB_HUMAN). Do NOT use UniProt entry names like ‘MEIOB_HUMAN’ - they will cause API errors. To find UniProt accession from a gene/protein name, use UniProt_search (e.g., query=’gene:MEIOB’ organism=’human’) or UniProt_id_mapping for ID conversion. Returns lightweight information such as sequence length, coverage, confidence scores, experimental method, resolution, oligomeric state, and structural entities. 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 (e.g., ‘Q5SWX9’). Do NOT use entry names like ‘MEIOB_HUMAN’. To find accession from gene name: use UniProt_search or UniProt_id_mapping.

Example Usage:

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