search-disease-proteins
Find proteins associated with specific diseases to support research and analysis of disease mechanisms and potential therapeutic targets.
Instructions
Search for proteins related to a disease
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| disease | Yes | Disease name (e.g., 'covid', 'alzheimer's') |
Implementation Reference
- Main handler function that executes the tool: searches RCSB PDB API for disease-related protein structures, fetches details for top results, handles fallback search, and returns formatted text output.
export async function searchDiseaseProteins({ disease }: { disease: string }, extra: RequestHandlerExtra): Promise<CallToolResult> { console.error(`DEBUG: Processing search-disease-proteins request for disease: ${disease}`); // Build a proper search query based on the curl example const searchQuery = { query: { type: "group", nodes: [ { type: "group", nodes: [ { type: "group", nodes: [ { type: "terminal", service: "full_text", parameters: { value: disease } } ], logical_operator: "and" } ], logical_operator: "and", label: "full_text" } ], logical_operator: "and" }, return_type: "entry", request_options: { paginate: { start: 0, rows: 25 }, results_content_type: [ "experimental" ], sort: [ { sort_by: "score", direction: "desc" } ], scoring_strategy: "combined" } }; console.error(`DEBUG: Using POST request to search API`); // Make a POST request with the properly structured query const searchData = await makeApiRequest(RCSB_PDB_SEARCH_API, 'POST', searchQuery) as SearchResponse; if (!searchData || !searchData.result_set) { return { content: [ { type: "text", text: `Failed to search for proteins related to: ${disease}. The search API might be temporarily unavailable.`, }, ], }; } // Check if we have results const results = searchData.result_set || []; console.error(`DEBUG: Found ${results.length} results for disease: ${disease}`); if (results.length === 0) { // Try alternative search with broader criteria const altSearchQuery = { query: { type: "group", nodes: [ { type: "group", nodes: [ { type: "terminal", service: "text", parameters: { attribute: "text", operator: "contains_phrase", value: disease } } ], logical_operator: "and" } ], logical_operator: "and" }, return_type: "entry", request_options: { paginate: { start: 0, rows: 25 }, sort: [ { sort_by: "score", direction: "desc" } ] } }; console.error(`DEBUG: No results with specific search, trying broader search with POST request`); const altSearchData = await makeApiRequest(RCSB_PDB_SEARCH_API, 'POST', altSearchQuery) as SearchResponse; if (!altSearchData || !altSearchData.result_set || altSearchData.result_set.length === 0) { return { content: [ { type: "text", text: `No proteins found related to: ${disease}. Try using a different disease name or more general terms.`, }, ], }; } const altResults = altSearchData.result_set; console.error(`DEBUG: Found ${altResults.length} results with broader search`); let resultsText = `Found ${altResults.length} proteins that might be related to: "${disease}"\n\n`; // Process the alternative results const topResults = altResults.slice(0, 5); for (const result of topResults) { const pdbId = result.identifier; console.error(`DEBUG: Fetching details for PDB ID: ${pdbId}`); const structureUrl = `${RCSB_PDB_DATA_API}/core/entry/${pdbId}`; const structureData = await makeApiRequest(structureUrl) as StructureData; if (!structureData) { resultsText += `PDB ID: ${pdbId} (Error fetching details)\n---\n\n`; continue; } resultsText += `PDB ID: ${pdbId}\n`; resultsText += `Title: ${structureData?.struct?.title || "Unknown"}\n`; if (structureData?.rcsb_primary_citation) { const citation = structureData.rcsb_primary_citation; resultsText += `Publication: ${citation.title || "Unknown"} (${citation.journal_abbrev || "Unknown"}, ${citation.year || "Unknown"})\n`; } resultsText += "---\n\n"; } resultsText += "To analyze any of these structures in detail, you can use the analyze-active-site tool with the PDB ID."; return { content: [ { type: "text", text: resultsText, }, ], }; } let resultsText = `Found ${results.length} proteins related to: "${disease}"\n\n`; // Get detailed info for top 5 results const topResults = results.slice(0, 5); for (const result of topResults) { const pdbId = result.identifier; console.error(`DEBUG: Fetching details for PDB ID: ${pdbId}`); const structureUrl = `${RCSB_PDB_DATA_API}/core/entry/${pdbId}`; const structureData = await makeApiRequest(structureUrl) as StructureData; if (!structureData) { resultsText += `PDB ID: ${pdbId} (Error fetching details)\n---\n\n`; continue; } resultsText += `PDB ID: ${pdbId}\n`; resultsText += `Title: ${structureData?.struct?.title || "Unknown"}\n`; if (structureData?.rcsb_primary_citation) { const citation = structureData.rcsb_primary_citation; resultsText += `Publication: ${citation.title || "Unknown"} (${citation.journal_abbrev || "Unknown"}, ${citation.year || "Unknown"})\n`; } resultsText += "---\n\n"; } // Add note about how to analyze structures resultsText += "To analyze any of these structures in detail, you can use the analyze-active-site tool with the PDB ID."; return { content: [ { type: "text", text: resultsText, }, ], }; } - Input schema using Zod to validate the 'disease' parameter.
export const searchDiseaseProteinsSchema = { disease: z.string().describe("Disease name (e.g., 'covid', 'alzheimer's')"), }; - src/server/index.ts:34-40 (registration)Registers the tool on the MCP server with name, description, schema, and handler.
// Register the search-disease-proteins tool server.tool( "search-disease-proteins", "Search for proteins related to a disease", searchDiseaseProteinsSchema, searchDiseaseProteins );