ChEMBL-MCP-Server

Overview

The ChEMBL-MCP-Server is a sophisticated integration between the Model Context Protocol and the ChEMBL chemical database, enabling AI assistants to perform complex chemical informatics tasks. It offers extensive functionality across chemical search, target analysis, bioactivity data, drug development, and chemical property analysis. The server implements proper MCP communication via stdio and includes comprehensive error handling, API integration, and both regular and batch processing capabilities.

Try asking AI

After installing, here are 5 things you can ask your AI assistant:

• search_compoundsquery: string, limit?: number, offset?: number

  Search the ChEMBL database for compounds by name, synonym, or identifier.

  Try:Find compounds similar to aspirinTry:Search for compounds with the name 'paracetamol'
• get_compound_infochembl_id: string

  Get detailed information for a specific compound by ChEMBL ID.

  Try:Get detailed information about CHEMBL25Try:Retrieve properties for aspirin using its ChEMBL ID
• search_targetsquery: string, target_type?: string, organism?: string, limit?: number

  Search for biological targets by name or type.

  Try:Find dopamine receptor targets in humansTry:Search for targets related to cancer
• search_activitiestarget_chembl_id?: string, assay_chembl_id?: string, molecule_chembl_id?: string, activity_type?: string, limit?: number

  Search bioactivity measurements and assay results.

  Try:Find IC50 values for compound CHEMBL25Try:Search for all activities against target CHEMBL2095173
• batch_compound_lookupchembl_ids: string[]

  Process multiple ChEMBL IDs efficiently.

  Try:Get information for multiple compounds: CHEMBL25, CHEMBL59, CHEMBL1642Try:Batch lookup for 10 different compounds
• search_by_inchiinchi_key?: string, inchi_string?: string

  Find compounds by InChI key or InChI string.

  Try:Find compounds with this InChI key: ...Try:Search for compounds matching this InChI string
• get_compound_structurechembl_id: string, format: string

  Retrieve chemical structures in various formats.

  Try:Get structure of aspirin in SMILES formatTry:Retrieve MOL file structure for CHEMBL25
• search_similar_compoundschembl_id: string, similarity_threshold: number

  Find chemically similar compounds using Tanimoto similarity.

  Try:Find compounds similar to aspirin with 0.8 similarityTry:Search for compounds similar to CHEMBL25 with 0.7 threshold
• get_target_infochembl_id: string

  Get detailed target information by ChEMBL target ID.

  Try:Get detailed information for target CHEMBL2095173Try:Retrieve properties for a specific target ID
• get_target_compoundschembl_id: string

  Get compounds tested against specific targets.

  Try:Find compounds tested against target CHEMBL2095173Try:Get all compounds that interact with a specific target
• search_by_activity_typeactivity_type: string, min_value?: number, max_value?: number

  Find bioactivity data by activity type and value range.

  Try:Find all IC50 values between 1 and 100 nMTry:Search for Ki values less than 10 micromolar
• get_dose_responsechembl_id: string

  Get dose-response data and activity profiles.

  Try:Get dose-response data for CHEMBL25Try:Retrieve activity profiles for a specific compound

Comparable tools

Installation

git clone <repository-url>
cd chembl-server

npm install

npm run build

{
  "mcpServers": {
    "chembl": {
      "command": "node",
      "args": ["/path/to/chembl-server/build/index.js"],
      "env": {}
    }
  }
}

FAQ

Is this server officially affiliated with ChEMBL?

No, this is an unofficial MCP server developed by Augmented Nature that provides access to the ChEMBL database via its REST API.

What types of chemical properties can be analyzed?

The server provides tools for ADMET analysis, molecular descriptors, solubility prediction, and drug-likeness assessment using metrics like Lipinski's Rule of Five.

Compare ChEMBL-MCP-Server with