AlphaFold MCP Server

Instructions

Implementation Reference

• src/index.ts:996-1053 (handler)

  The handler function that executes the 'analyze_confidence_regions' tool. It fetches AlphaFold prediction data for the given UniProt ID and performs analysis to identify confidence regions (very high, confident, low) with mock data based on sequence length.
  private async handleAnalyzeConfidenceRegions(args: any) { if (!isValidConfidenceArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid confidence analysis arguments'); } try { const response = await this.apiClient.get(`/prediction/${args.uniprotId}`); const structures = response.data; if (!structures || structures.length === 0) { return { content: [ { type: 'text', text: `No structure available for ${args.uniprotId}`, }, ], }; } const structure = structures[0]; const sequenceLength = structure.uniprotSequence.length; // Mock confidence analysis const regions = { veryHighConfidence: { start: 1, end: Math.floor(sequenceLength * 0.3), avgScore: 95 }, confident: { start: Math.floor(sequenceLength * 0.3) + 1, end: Math.floor(sequenceLength * 0.7), avgScore: 80 }, lowConfidence: { start: Math.floor(sequenceLength * 0.7) + 1, end: sequenceLength, avgScore: 60 }, }; return { content: [ { type: 'text', text: JSON.stringify({ uniprotId: args.uniprotId, confidenceRegions: regions, analysis: { highConfidencePercentage: 30, mediumConfidencePercentage: 40, lowConfidencePercentage: 30, }, }, null, 2), }, ], }; } catch (error) { return { content: [ { type: 'text', text: `Error analyzing confidence regions: ${error instanceof Error ? error.message : 'Unknown error'}`, }, ], isError: true, }; } }
• src/index.ts:432-442 (schema)

  The input schema definition for the 'analyze_confidence_regions' tool, specifying the required 'uniprotId' parameter.
  { name: 'analyze_confidence_regions', description: 'Analyze confidence score distribution and identify high/low confidence regions', inputSchema: { type: 'object', properties: { uniprotId: { type: 'string', description: 'UniProt accession' }, }, required: ['uniprotId'], }, },
• src/index.ts:595-596 (registration)

  The dispatch case in the CallToolRequestSchema handler that routes calls to 'analyze_confidence_regions' to its handler function.
  case 'analyze_confidence_regions': return this.handleAnalyzeConfidenceRegions(args);
• src/index.ts:344-572 (registration)

  The tool registration in ListToolsRequestSchema where 'analyze_confidence_regions' is listed among available tools with its schema.
  this.server.setRequestHandler(ListToolsRequestSchema, async () => ({ tools: [ // Core Structure Tools { name: 'get_structure', description: 'Get AlphaFold structure prediction for a specific UniProt ID', inputSchema: { type: 'object', properties: { uniprotId: { type: 'string', description: 'UniProt accession (e.g., P21359, Q8N726)' }, format: { type: 'string', enum: ['pdb', 'cif', 'bcif', 'json'], description: 'Output format (default: json)' }, }, required: ['uniprotId'], }, }, { name: 'download_structure', description: 'Download AlphaFold structure file in specified format', inputSchema: { type: 'object', properties: { uniprotId: { type: 'string', description: 'UniProt accession' }, format: { type: 'string', enum: ['pdb', 'cif', 'bcif'], description: 'File format (default: pdb)' }, }, required: ['uniprotId'], }, }, { name: 'check_availability', description: 'Check if AlphaFold structure prediction is available for a UniProt ID', inputSchema: { type: 'object', properties: { uniprotId: { type: 'string', description: 'UniProt accession to check' }, }, required: ['uniprotId'], }, }, // Search & Discovery Tools { name: 'search_structures', description: 'Search for available AlphaFold structures by protein name or gene', inputSchema: { type: 'object', properties: { query: { type: 'string', description: 'Search term (protein name, gene name, etc.)' }, organism: { type: 'string', description: 'Filter by organism (optional)' }, size: { type: 'number', description: 'Number of results (1-100, default: 25)', minimum: 1, maximum: 100 }, }, required: ['query'], }, }, { name: 'list_by_organism', description: 'List all available structures for a specific organism', inputSchema: { type: 'object', properties: { organism: { type: 'string', description: 'Organism name (e.g., "Homo sapiens", "Escherichia coli")' }, size: { type: 'number', description: 'Number of results (1-100, default: 50)', minimum: 1, maximum: 100 }, }, required: ['organism'], }, }, { name: 'get_organism_stats', description: 'Get statistics about AlphaFold coverage for an organism', inputSchema: { type: 'object', properties: { organism: { type: 'string', description: 'Organism name' }, }, required: ['organism'], }, }, // Confidence & Quality Tools { name: 'get_confidence_scores', description: 'Get per-residue confidence scores for a structure prediction', inputSchema: { type: 'object', properties: { uniprotId: { type: 'string', description: 'UniProt accession' }, threshold: { type: 'number', description: 'Confidence threshold (0-100, optional)', minimum: 0, maximum: 100 }, }, required: ['uniprotId'], }, }, { name: 'analyze_confidence_regions', description: 'Analyze confidence score distribution and identify high/low confidence regions', inputSchema: { type: 'object', properties: { uniprotId: { type: 'string', description: 'UniProt accession' }, }, required: ['uniprotId'], }, }, { name: 'get_prediction_metadata', description: 'Get metadata about the prediction including version, date, and quality metrics', inputSchema: { type: 'object', properties: { uniprotId: { type: 'string', description: 'UniProt accession' }, }, required: ['uniprotId'], }, }, // Batch Processing Tools { name: 'batch_structure_info', description: 'Get structure information for multiple proteins simultaneously', inputSchema: { type: 'object', properties: { uniprotIds: { type: 'array', items: { type: 'string' }, description: 'Array of UniProt accessions (max 50)', minItems: 1, maxItems: 50 }, format: { type: 'string', enum: ['json', 'summary'], description: 'Output format (default: json)' }, }, required: ['uniprotIds'], }, }, { name: 'batch_download', description: 'Download multiple structure files', inputSchema: { type: 'object', properties: { uniprotIds: { type: 'array', items: { type: 'string' }, description: 'Array of UniProt accessions (max 20)', minItems: 1, maxItems: 20 }, format: { type: 'string', enum: ['pdb', 'cif'], description: 'File format (default: pdb)' }, }, required: ['uniprotIds'], }, }, { name: 'batch_confidence_analysis', description: 'Analyze confidence scores for multiple proteins', inputSchema: { type: 'object', properties: { uniprotIds: { type: 'array', items: { type: 'string' }, description: 'Array of UniProt accessions (max 30)', minItems: 1, maxItems: 30 }, }, required: ['uniprotIds'], }, }, // Comparative Analysis Tools { name: 'compare_structures', description: 'Compare multiple AlphaFold structures for analysis', inputSchema: { type: 'object', properties: { uniprotIds: { type: 'array', items: { type: 'string' }, description: 'Array of UniProt accessions to compare (2-10)', minItems: 2, maxItems: 10 }, }, required: ['uniprotIds'], }, }, { name: 'find_similar_structures', description: 'Find AlphaFold structures similar to a given protein', inputSchema: { type: 'object', properties: { uniprotId: { type: 'string', description: 'Reference UniProt accession' }, organism: { type: 'string', description: 'Filter by organism (optional)' }, }, required: ['uniprotId'], }, }, // Coverage & Completeness Tools { name: 'get_coverage_info', description: 'Get information about sequence coverage in the AlphaFold prediction', inputSchema: { type: 'object', properties: { uniprotId: { type: 'string', description: 'UniProt accession' }, }, required: ['uniprotId'], }, }, { name: 'validate_structure_quality', description: 'Validate and assess the overall quality of an AlphaFold prediction', inputSchema: { type: 'object', properties: { uniprotId: { type: 'string', description: 'UniProt accession' }, }, required: ['uniprotId'], }, }, // Export & Integration Tools { name: 'export_for_pymol', description: 'Export structure data formatted for PyMOL visualization', inputSchema: { type: 'object', properties: { uniprotId: { type: 'string', description: 'UniProt accession' }, includeConfidence: { type: 'boolean', description: 'Include confidence score coloring (default: true)' }, }, required: ['uniprotId'], }, }, { name: 'export_for_chimerax', description: 'Export structure data formatted for ChimeraX visualization', inputSchema: { type: 'object', properties: { uniprotId: { type: 'string', description: 'UniProt accession' }, includeConfidence: { type: 'boolean', description: 'Include confidence score coloring (default: true)' }, }, required: ['uniprotId'], }, }, { name: 'get_api_status', description: 'Check AlphaFold API status and database statistics', inputSchema: { type: 'object', properties: {}, required: [], }, }, ], }));
• src/index.ts:122-132 (helper)

  Validation function for confidence-related tool arguments, used by 'analyze_confidence_regions' to validate input parameters.
  const isValidConfidenceArgs = ( args: any ): args is { uniprotId: string; threshold?: number } => { return ( typeof args === 'object' && args !== null && typeof args.uniprotId === 'string' && args.uniprotId.length > 0 && (args.threshold === undefined || (typeof args.threshold === 'number' && args.threshold >= 0 && args.threshold <= 100)) ); };