SureChEMBL MCP Server

Instructions

Implementation Reference

• src/index.ts:1063-1118 (handler)

  The handler function executing the tool logic. It fetches the reference chemical and returns a mock similarity search result with suggestions since direct similarity search is not supported.

  private async handleSearchSimilarStructures(args: any) {
    if (!args || typeof args.reference_id !== 'string') {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid reference chemical ID');
    }
  
    try {
      // Get the reference chemical first
      const refResponse = await this.apiClient.get(`/chemical/id/${args.reference_id}`);
      const refChemical = refResponse.data.data?.[0];
  
      if (!refChemical) {
        throw new Error('Reference chemical not found');
      }
  
      // Since SureChEMBL doesn't have direct similarity search, we'll provide a mock implementation
      // that explains the limitation and suggests alternatives
      const similarityResult = {
        reference_chemical: {
          id: args.reference_id,
          name: refChemical.name,
          smiles: refChemical.smiles,
          molecular_weight: refChemical.mol_weight
        },
        search_parameters: {
          threshold: args.threshold || 0.7,
          limit: args.limit || 25
        },
        message: 'Direct similarity search not available in SureChEMBL API',
        suggestions: [
          'Use chemical name variations to find related compounds',
          'Search by molecular weight ranges',
          'Use external cheminformatics tools for similarity search',
          'Try searching by chemical class or functional groups'
        ],
        alternative_searches: {
          by_name_fragments: `Try searching for fragments of "${refChemical.name}"`,
          by_molecular_weight: `Search for compounds with molecular weight around ${refChemical.mol_weight}`,
          by_chemical_class: 'Search for compounds in the same chemical class'
        }
      };
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(similarityResult, null, 2),
          },
        ],
      };
    } catch (error) {
      throw new McpError(
        ErrorCode.InternalError,
        `Failed to search similar structures: ${error instanceof Error ? error.message : 'Unknown error'}`
      );
    }
  }

• src/index.ts:513-521 (schema)

  Input schema defining parameters for the search_similar_structures tool.

  inputSchema: {
    type: 'object',
    properties: {
      reference_id: { type: 'string', description: 'Reference chemical ID for similarity search' },
      threshold: { type: 'number', description: 'Similarity threshold (0.0-1.0, default: 0.7)', minimum: 0.0, maximum: 1.0 },
      limit: { type: 'number', description: 'Number of results to return (1-100, default: 25)', minimum: 1, maximum: 100 },
    },
    required: ['reference_id'],
  },

• src/index.ts:510-522 (registration)

  Tool registration object including name, description, and schema in the tools array.

  {
    name: 'search_similar_structures',
    description: 'Find structurally similar chemicals using similarity search',
    inputSchema: {
      type: 'object',
      properties: {
        reference_id: { type: 'string', description: 'Reference chemical ID for similarity search' },
        threshold: { type: 'number', description: 'Similarity threshold (0.0-1.0, default: 0.7)', minimum: 0.0, maximum: 1.0 },
        limit: { type: 'number', description: 'Number of results to return (1-100, default: 25)', minimum: 1, maximum: 100 },
      },
      required: ['reference_id'],
    },
  },

• src/index.ts:574-575 (registration)

  Switch case in the request handler dispatching to the tool handler.

  case 'search_similar_structures':
    return await this.handleSearchSimilarStructures(args);