UniProt MCP Server

Instructions

Implementation Reference

• src/index.ts:991-1033 (handler)

  The handler function for the 'compare_proteins' tool. Validates input, fetches UniProt data for each accession, extracts key properties (accession, name, organism, sequence length, molecular weight, feature count, domain count), compiles a comparison array, and returns it as JSON.

  private async handleCompareProteins(args: any) {
    if (!isValidCompareProteinsArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid compare proteins arguments');
    }
  
    try {
      const comparisons = [];
      for (const accession of args.accessions) {
        const response = await this.apiClient.get(`/uniprotkb/${accession}`, {
          params: { format: 'json' },
        });
        const protein = response.data;
        comparisons.push({
          accession: protein.primaryAccession,
          name: protein.uniProtkbId,
          organism: protein.organism?.scientificName,
          length: protein.sequence?.length,
          mass: protein.sequence?.molWeight,
          features: protein.features?.length || 0,
          domains: protein.features?.filter((f: any) => f.type === 'Domain').length || 0,
        });
      }
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify({ comparison: comparisons }, null, 2),
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: `Error comparing proteins: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
        isError: true,
      };
    }
  }

• src/index.ts:739-740 (registration)

  Registers the handler for 'compare_proteins' in the CallToolRequestSchema switch statement.

  case 'compare_proteins':
    return this.handleCompareProteins(args);

• src/index.ts:464-474 (registration)

  Registers the 'compare_proteins' tool in the ListToolsRequestSchema response, including name, description, and input schema.

    name: 'compare_proteins',
    description: 'Compare multiple proteins side-by-side with sequence and feature comparison',
    inputSchema: {
      type: 'object',
      properties: {
        accessions: { type: 'array', items: { type: 'string' }, description: 'Array of UniProt accession numbers (2-10)', minItems: 2, maxItems: 10 },
        format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' },
      },
      required: ['accessions'],
    },
  },

• src/index.ts:116-128 (schema)

  Input validation type guard function for 'compare_proteins' tool arguments, checking accessions array (2-10 strings) and optional format.

  const isValidCompareProteinsArgs = (
    args: any
  ): args is { accessions: string[]; format?: string } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      Array.isArray(args.accessions) &&
      args.accessions.length > 1 &&
      args.accessions.length <= 10 &&
      args.accessions.every((acc: any) => typeof acc === 'string' && acc.length > 0) &&
      (args.format === undefined || ['json', 'tsv'].includes(args.format))
    );
  };