AlphaFold MCP Server

Instructions

Implementation Reference

• src/index.ts:741-780 (handler)

  The handler function for the 'check_availability' tool. It validates input, queries the AlphaFold API endpoint `/prediction/{uniprotId}`, checks if structures exist, and returns a JSON object with availability status, structure count, latest version, and model creation date. Handles errors by returning unavailable status with error message.

  private async handleCheckAvailability(args: any) {
    if (!isValidUniProtArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid availability check arguments');
    }
  
    try {
      const response = await this.apiClient.get(`/prediction/${args.uniprotId}`);
      const structures = response.data;
  
      const availability = {
        uniprotId: args.uniprotId,
        available: structures && structures.length > 0,
        structureCount: structures ? structures.length : 0,
        latestVersion: structures && structures.length > 0 ? structures[0].latestVersion : null,
        modelCreatedDate: structures && structures.length > 0 ? structures[0].modelCreatedDate : null,
      };
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(availability, null, 2),
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify({
              uniprotId: args.uniprotId,
              available: false,
              error: error instanceof Error ? error.message : 'Unknown error'
            }, null, 2),
          },
        ],
      };
    }
  }

• src/index.ts:375-380 (schema)

  Input schema definition for the 'check_availability' tool, specifying a required 'uniprotId' string parameter.

    type: 'object',
    properties: {
      uniprotId: { type: 'string', description: 'UniProt accession to check' },
    },
    required: ['uniprotId'],
  },

• src/index.ts:583-584 (registration)

  Registration/dispatch in the CallToolRequestSchema switch statement that routes calls to the 'check_availability' handler.

  case 'check_availability':
    return this.handleCheckAvailability(args);

• src/index.ts:372-381 (registration)

  Tool registration in the ListToolsRequestSchema response, defining name, description, and input schema.

    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'],
    },
  },

• src/index.ts:58-68 (helper)

  Helper validation function used by check_availability (and others) to validate uniprotId input parameter.

  const isValidUniProtArgs = (
    args: any
  ): args is { uniprotId: string; format?: 'pdb' | 'cif' | 'bcif' | 'json' } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      typeof args.uniprotId === 'string' &&
      args.uniprotId.length > 0 &&
      (args.format === undefined || ['pdb', 'cif', 'bcif', 'json'].includes(args.format))
    );
  };