find_similar_structures
Find AlphaFold structures similar to a given protein.
How to use it
find_similar_structures is exposed by the AlphaFold MCP Server MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), and the find_similar_structures tool becomes available to the model automatically. See the full listing for setup details and every tool this server provides.
FULL ALPHAFOLD MCP SERVER LISTINGOther tools in AlphaFold MCP Server (26)
Analyze confidence score distribution and identify high/low confidence regions.
Analyze confidence scores for multiple proteins.
Download multiple structure files.
Get structure information for multiple proteins simultaneously.
Check if AlphaFold structure prediction is available for a UniProt ID.
Compare multiple AlphaFold structures for analysis.
Download AlphaFold structure file in specified format.
Export structure data formatted for ChimeraX visualization.
Export structure data formatted for PyMOL visualization.
(optional): Output format - "pdb", "cif", "bcif", or "json" (default: "json")
Check AlphaFold API status and database statistics.
Get per-residue confidence scores for a structure prediction.
Get information about sequence coverage in the AlphaFold prediction.
Get statistics about AlphaFold coverage for an organism.
Get metadata about the prediction including version, date, and quality metrics.
Retrieve AlphaFold structure prediction for a specific UniProt ID.
(optional): Include confidence score coloring (default: true)
List all available structures for a specific organism.
(optional): Filter by organism
(required): Search term (protein name, gene name, etc.)
Search for available AlphaFold structures by protein name or gene.
(optional): Number of results (1-100, default: 25)
(optional): Confidence threshold (0-100)
(required): UniProt accession (e.g., "P21359", "Q8N726")
(required): Array of UniProt accessions (max 50)
Validate and assess the overall quality of an AlphaFold prediction.