ChEMBL MCP Server

Instructions

Implementation Reference

• src/index.ts:1584-1674 (handler)

  The handler function for the 'predict_solubility' tool. Fetches molecule data from ChEMBL API using chembl_id, extracts properties like alogp, psa, etc., applies simple rules to predict solubility class and permeability, and returns formatted JSON response.

  private async handlePredictSolubility(args: any) {
    if (!args || (!args.chembl_id && !args.smiles)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid solubility prediction arguments');
    }
  
    try {
      let molecule;
      if (args.chembl_id) {
        const response = await this.apiClient.get(`/molecule/${args.chembl_id}.json`);
        molecule = response.data;
      } else {
        return {
          content: [
            {
              type: 'text',
              text: JSON.stringify({
                message: 'SMILES-based solubility prediction requires ChEMBL ID',
                smiles: args.smiles,
              }, null, 2),
            },
          ],
        };
      }
  
      const props = molecule.molecule_properties || {};
  
      // Predict solubility based on molecular properties
      const logp = props.alogp || 0;
      const psa = props.psa || 0;
      const mw = props.full_mwt || props.molecular_weight || 0;
      const hbd = props.hbd || 0;
      const hba = props.hba || 0;
  
      // Simple solubility prediction model
      let solubilityClass = 'Moderate';
      let permeability = 'Moderate';
  
      if (logp < 0 && psa > 100) {
        solubilityClass = 'High';
        permeability = 'Low';
      } else if (logp > 5 || psa < 40) {
        solubilityClass = 'Low';
        permeability = 'High';
      } else if (logp > 3 && psa < 70) {
        solubilityClass = 'Low-Moderate';
        permeability = 'High';
      } else if (logp < 2 && psa > 80) {
        solubilityClass = 'Moderate-High';
        permeability = 'Low-Moderate';
      }
  
      const solubilityPrediction = {
        chembl_id: molecule.molecule_chembl_id,
        aqueous_solubility: {
          predicted_class: solubilityClass,
          logp: logp,
          psa: psa,
          factors: {
            lipophilicity: logp > 3 ? 'High (reduces solubility)' : 'Moderate',
            polar_surface_area: psa > 100 ? 'High (increases solubility)' : 'Moderate',
            hydrogen_bonding: `${hbd} donors, ${hba} acceptors`,
          },
        },
        permeability: {
          predicted_class: permeability,
          assessment: this.assessPermeability(props),
        },
        molecular_properties: {
          molecular_weight: mw,
          alogp: logp,
          psa: psa,
          hbd: hbd,
          hba: hba,
        },
      };
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(solubilityPrediction, null, 2),
          },
        ],
      };
    } catch (error) {
      throw new McpError(
        ErrorCode.InternalError,
        `Failed to predict solubility: ${error instanceof Error ? error.message : 'Unknown error'}`
      );
    }
  }

• src/index.ts:661-670 (schema)

  Input schema definition for the predict_solubility tool, allowing optional chembl_id or smiles.

  name: 'predict_solubility',
  description: 'Predict aqueous solubility and permeability properties',
  inputSchema: {
    type: 'object',
    properties: {
      chembl_id: { type: 'string', description: 'ChEMBL compound ID' },
      smiles: { type: 'string', description: 'SMILES string (alternative to ChEMBL ID)' },
    },
    required: [],
  },

• src/index.ts:792-792 (registration)

  Registration of the predict_solubility handler in the CallToolRequestSchema switch statement.

  return await this.handlePredictSolubility(args);

• src/index.ts:1676-1686 (helper)

  Helper function used by the handler to assess membrane permeability based on PSA and logP.

  private assessPermeability(props: any): string {
    const psa = props.psa || 0;
    const logp = props.alogp || 0;
  
    if (psa < 90 && logp > 0 && logp < 5) {
      return 'Good membrane permeability predicted';
    } else if (psa > 140 || logp < -1) {
      return 'Poor membrane permeability predicted';
    }
    return 'Moderate membrane permeability predicted';
  }