AlphaFold MCP Server

Instructions

Implementation Reference

• src/index.ts:1315-1372 (handler)

  The handler function that executes the 'compare_structures' tool. It validates input, fetches AlphaFold structure data for each UniProt ID, compiles comparison data (entryId, gene, organism, sequence length, coverage percentage, model date), handles errors per ID, and returns a JSON summary.

  private async handleCompareStructures(args: any) {
    if (!isValidCompareArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid compare structures arguments');
    }
  
    try {
      const comparisons = [];
  
      for (const uniprotId of args.uniprotIds) {
        try {
          const response = await this.apiClient.get(`/prediction/${uniprotId}`);
          const structures = response.data;
  
          if (structures && structures.length > 0) {
            const structure = structures[0];
            comparisons.push({
              uniprotId,
              entryId: structure.entryId,
              gene: structure.gene,
              organism: structure.organismScientificName,
              sequenceLength: structure.uniprotSequence.length,
              coverage: ((structure.uniprotEnd - structure.uniprotStart + 1) / structure.uniprotSequence.length) * 100,
              modelCreatedDate: structure.modelCreatedDate,
            });
          } else {
            comparisons.push({
              uniprotId,
              error: 'No structure found',
            });
          }
        } catch (error) {
          comparisons.push({
            uniprotId,
            error: error instanceof Error ? error.message : 'Unknown error',
          });
        }
      }
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify({ structureComparison: comparisons }, null, 2),
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: `Error comparing structures: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
        isError: true,
      };
    }
  }

• src/index.ts:491-501 (registration)

  Registration of the 'compare_structures' tool in the ListTools response, including name, description, and input schema definition.

  {
    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'],
    },
  },

• src/index.ts:607-608 (registration)

  Handler dispatch in the CallToolRequest switch statement that routes 'compare_structures' calls to the implementation method.

  case 'compare_structures':
    return this.handleCompareStructures(args);

• src/index.ts:109-120 (schema)

  Input validation type guard for 'compare_structures' tool arguments, ensuring uniprotIds is a non-empty array of 2-10 valid strings.

  const isValidCompareArgs = (
    args: any
  ): args is { uniprotIds: string[] } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      Array.isArray(args.uniprotIds) &&
      args.uniprotIds.length >= 2 &&
      args.uniprotIds.length <= 10 &&
      args.uniprotIds.every((id: any) => typeof id === 'string' && id.length > 0)
    );
  };