A comprehensive Model Context Protocol (MCP) server that provides access to the AlphaFold Protein Structure Database through a rich set of tools and resources for protein structure prediction analysis.
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Highlight AIRetrieve AlphaFold structure prediction for a specific UniProt ID. Parameters: uniprotId (required), format (optional: 'pdb', 'cif', 'bcif', or 'json', default: 'json')
Download AlphaFold structure file in specified format. Parameters: uniprotId (required), format (optional: 'pdb', 'cif', or 'bcif', default: 'pdb')
Check if AlphaFold structure prediction is available for a UniProt ID. Parameters: uniprotId (required)
Search for available AlphaFold structures by protein name or gene. Parameters: query (required), organism (optional), size (optional: 1-100, default: 25)
List all available structures for a specific organism. Parameters: organism (required), size (optional: 1-100, default: 50)
Get statistics about AlphaFold coverage for an organism. Parameters: organism (required)
Get per-residue confidence scores for a structure prediction. Parameters: uniprotId (required), threshold (optional: 0-100)
Analyze confidence score distribution and identify high/low confidence regions. Parameters: uniprotId (required)
Get metadata about the prediction including version, date, and quality metrics. Parameters: uniprotId (required)
Get structure information for multiple proteins simultaneously. Parameters: uniprotIds (required: Array of UniProt accessions, max 50), format (optional: 'json' or 'summary', default: 'json')
Download multiple structure files. Parameters: uniprotIds (required: Array of UniProt accessions, max 20), format (optional: 'pdb' or 'cif', default: 'pdb')
Analyze confidence scores for multiple proteins. Parameters: uniprotIds (required: Array of UniProt accessions, max 30)
Compare multiple AlphaFold structures for analysis. Parameters: uniprotIds (required: Array of UniProt accessions to compare, 2-10)
Find AlphaFold structures similar to a given protein. Parameters: uniprotId (required), organism (optional)
Get information about sequence coverage in the AlphaFold prediction. Parameters: uniprotId (required)
Validate and assess the overall quality of an AlphaFold prediction. Parameters: uniprotId (required)
Export structure data formatted for PyMOL visualization. Parameters: uniprotId (required), includeConfidence (optional: default true)
Export structure data formatted for ChimeraX visualization. Parameters: uniprotId (required), includeConfidence (optional: default true)
Check AlphaFold API status and database statistics. Parameters: None
