bc_get_alphafold_info_by_protein_symbol

Retrieve AlphaFold protein structure predictions by converting protein symbols to UniProt IDs and fetching detailed structural data including PDB/CIF files and confidence scores.

Instructions

Query AlphaFold database using protein name. First converts protein symbol to UniProt ID, then fetches structure predictions.

Returns: dict: AlphaFold prediction data including PDB/CIF file URLs, confidence scores, and metadata or error message.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`protein_symbol`	Yes	Gene/protein name (e.g., 'SYNPO')
`species`	No	Taxonomy ID (e.g., '9606' for human)	9606

Implementation Reference

src/biocontext_kb/core/alphafold/_get_alphafold_info_by_protein_symbol.py:15-48 (handler)

The core handler function for the 'bc_get_alphafold_info_by_protein_symbol' tool. It resolves the protein symbol to a UniProt ID using another tool, then fetches AlphaFold structure predictions. Includes input schema via Pydantic Annotated Fields.

@core_mcp.tool()
def get_alphafold_info_by_protein_symbol(
    protein_symbol: Annotated[str, Field(description="Gene/protein name (e.g., 'SYNPO')")],
    species: Annotated[
        str,
        Field(description="Taxonomy ID (e.g., '9606' for human)"),
    ] = "9606",
) -> dict:
    """Query AlphaFold database using protein name. First converts protein symbol to UniProt ID, then fetches structure predictions.

    Returns:
        dict: AlphaFold prediction data including PDB/CIF file URLs, confidence scores, and metadata or error message.
    """
    # Get the UniProt Id from the protein_symbol
    try:
        uniprot_id = get_uniprot_id_by_protein_symbol.fn(protein_symbol, species)

        if uniprot_id:
            result = get_alphafold_info_by_uniprot_id(uniprot_id)
            if isinstance(result, dict) and "error" in result:
                return {"error": result["error"]}
            elif isinstance(result, list) and len(result) > 0:
                # If result is a list, return the first item
                return result[0]
            elif isinstance(result, dict):
                # If result is a dict, return it directly
                return result
            else:
                return {"error": "Unexpected result format from AlphaFold query"}
        else:
            return {"error": "No results found for the given protein name"}
    except requests.exceptions.RequestException as e:
        return {"error": f"Failed to fetch AlphaFold info: {e!s}"}

src/biocontext_kb/core/alphafold/_get_alphafold_info_by_uniprot_id.py:8-33 (helper)

Helper function called by the handler to query AlphaFold API directly using UniProt ID.

def get_alphafold_info_by_uniprot_id(
    uniprot_id: Annotated[str, Field(description="UniProt protein ID (e.g., 'P62258')")],
) -> dict:
    """Query AlphaFold database for protein structure data.

    Returns:
        dict: AlphaFold prediction data including PDB/CIF file URLs, confidence scores, and metadata or error message.
    """
    # Ensure the UniProt ID is in uppercase
    uniprot_id = uniprot_id.upper()

    # Validate the UniProt ID format
    if not re.match(r"^[A-Z0-9]{6}$", uniprot_id):
        return {"error": "Invalid UniProt ID format"}

    # Construct the URL for AlphaFold database query
    url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}"

    try:
        # Make the request and get the response
        response = requests.get(url)
        response.raise_for_status()
        return response.json()
    except requests.exceptions.RequestException as e:
        return {"error": f"Failed to fetch AlphaFold info: {e!s}"}

src/biocontext_kb/core/uniprot/_get_uniprot_id_by_protein_symbol.py:9-32 (helper)

Helper tool called by the main handler (via .fn()) to resolve protein symbol and species to UniProt ID using UniProt REST API.

@core_mcp.tool()
def get_uniprot_id_by_protein_symbol(
    protein_symbol: Annotated[str, Field(description="Gene or protein name to search for (e.g., 'SYNPO')")],
    species: Annotated[
        str,
        Field(description="Organism taxonomy ID (e.g., '9606' for human)"),
    ] = "9606",
) -> str | None:
    """Retrieve UniProt accession ID from protein name and species. Returns the primary accession or None if not found.

    Returns:
        str or None: UniProt accession ID string (e.g., 'P04637') or None if not found.
    """
    url = f"https://rest.uniprot.org/uniprotkb/search?query=protein_name:{protein_symbol}+AND+organism_id:{species}&format=json"

    response = requests.get(url)
    response.raise_for_status()
    data = response.json()

    if data["results"]:
        return data["results"][0]["primaryAccession"]

    return None

src/biocontext_kb/core/_server.py:3-6 (registration)
The FastMCP server instance 'core_mcp' with prefix 'BC' to which all tools including 'bc_get_alphafold_info_by_protein_symbol' are registered via decorators.
```
core_mcp = FastMCP(  # type: ignore
    "BC",
    instructions="Provides access to biomedical knowledge bases.",
)
```

BioContextAI Knowledgebase MCP