Unofficial ChEMBL MCP Server

Access the ChEMBL chemical database for drug discovery, chemical informatics, and bioactivity research using specialized tools via its REST API.

A comprehensive Model Context Protocol (MCP) server providing advanced access to the ChEMBL chemical database. This server offers 22 specialized tools enabling AI assistants and MCP clients to perform sophisticated drug discovery research, chemical informatics analysis, and bioactivity investigations directly through ChEMBL's REST API.

Core Chemical Search & Retrieval (5 tools)

- Compound Search: Search the ChEMBL database by compound name, synonym, or identifier
- Detailed Compound Info: Retrieve comprehensive compound information including structure, properties, and annotations
- InChI-based Search: Find compounds by InChI key or InChI string
- Structure Retrieval: Get chemical structure information in various formats (SMILES, InChI, MOL, SDF)
- Similarity Search: Find chemically similar compounds using Tanimoto similarity

Target Analysis & Drug Discovery (5 tools)

- Target Search: Search for biological targets by name or type
- Detailed Target Info: Retrieve comprehensive target information and annotations
- Target Compounds: Get compounds tested against specific targets
- UniProt Integration: Find ChEMBL targets by UniProt accession numbers
- Target Pathways: Associated biological pathways and mechanisms

- Activity Search: Search bioactivity measurements and assay results
- Detailed Assay Info: Get comprehensive assay protocols and conditions
- Activity Type Search: Find bioactivity data by specific activity type and value range
- Dose-Response Analysis: Get dose-response data and activity profiles
- Activity Comparison: Compare bioactivity data across multiple compounds or targets

Drug Development & Clinical Data (4 tools)

- Drug Search: Search for approved drugs and clinical candidates
- Drug Development Status: Get drug development status and clinical trial information
- Therapeutic Indications: Search for therapeutic indications and disease areas
- Mechanism of Action: Get mechanism of action and target interaction data

- ADMET Analysis: Analyze ADMET properties (Absorption, Distribution, Metabolism, Excretion, Toxicity)
- Molecular Descriptors: Calculate molecular descriptors and physicochemical properties
- Solubility Prediction: Predict aqueous solubility and permeability properties
- Drug-Likeness Assessment: Assess drug-likeness using Lipinski Rule of Five and other metrics

Advanced Search & Cross-References (4 tools)

- Substructure Search: Find compounds containing specific substructures
- Batch Processing: Process multiple ChEMBL IDs efficiently
- External References: Get links to external databases (PubChem, DrugBank, PDB, etc.)
- Advanced Search: Complex queries with multiple chemical and biological filters

- Direct access to ChEMBL data via URI templates for seamless integration

git clone <repository-url> cd chembl-server

For MCP client integration, you can use the container directly:

{ "mcpServers": { "chembl": { "command": "docker", "args": ["run", "-i", "chembl-mcp-server"], "env": {} } } }

The server is designed to run as an MCP server that communicates via stdio:

Add the server to your MCP client configuration (e.g., Claude Desktop):

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

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

- query(required): Search query (compound name, synonym, or identifier)
- limit(optional): Number of results to return (1-1000, default: 25)
- offset(optional): Number of results to skip (default: 0)

{ "query": "aspirin", "limit": 10 }

Get detailed information for a specific compound by ChEMBL ID.

- chembl_id(required): ChEMBL compound ID (e.g., CHEMBL25)

{ "chembl_id": "CHEMBL25" }

Search for biological targets by name or type.

- query(required): Target name or search query
- target_type(optional): Target type filter (e.g., SINGLE PROTEIN, PROTEIN COMPLEX)
- organism(optional): Organism filter
- limit(optional): Number of results to return (1-1000, default: 25)

{ "query": "dopamine receptor", "organism": "Homo sapiens", "limit": 5 }

Search bioactivity measurements and assay results.

- target_chembl_id(optional): ChEMBL target ID filter
- assay_chembl_id(optional): ChEMBL assay ID filter
- molecule_chembl_id(optional): ChEMBL compound ID filter
- activity_type(optional): Activity type (e.g., IC50, Ki, EC50)
- limit(optional): Number of results to return (1-1000, default: 25)

{ "target_chembl_id": "CHEMBL2095173", "activity_type": "IC50", "limit": 50 }

Process multiple ChEMBL IDs efficiently.

- chembl_ids(required): Array of ChEMBL compound IDs (1-50)

{ "chembl_ids": ["CHEMBL25", "CHEMBL59", "CHEMBL1642"] }

The server provides direct access to ChEMBL data through URI templates:

- URI:chembl://compound/{chembl_id}
- Description: Complete compound information for a ChEMBL ID
- Example:chembl://compound/CHEMBL25

- URI:chembl://target/{chembl_id}
- Description: Complete target information for a ChEMBL target ID
- Example:chembl://target/CHEMBL2095173

- URI:chembl://assay/{chembl_id}
- Description: Complete assay information for a ChEMBL assay ID
- Example:chembl://assay/CHEMBL1217643

- URI:chembl://activity/{activity_id}
- Description: Bioactivity measurement data for an activity ID
- Example:chembl://activity/12345678

- URI:chembl://search/{query}
- Description: Search results for compounds matching the query
- Example:chembl://search/aspirin

// Tool call { "tool": "search_compounds", "arguments": { "query": "aspirin", "limit": 5 } }

Retrieve comprehensive information about aspirin:

// Tool call { "tool": "get_compound_info", "arguments": { "chembl_id": "CHEMBL25" } }

Find compounds tested against dopamine receptors:

// Tool call { "tool": "search_targets", "arguments": { "query": "dopamine receptor D2", "organism": "Homo sapiens" } }

Search for IC50 data against a specific target:

// Tool call { "tool": "search_activities", "arguments": { "target_chembl_id": "CHEMBL2095173", "activity_type": "IC50", "limit": 100 } }

// Tool call { "tool": "batch_compound_lookup", "arguments": { "chembl_ids": ["CHEMBL25", "CHEMBL59", "CHEMBL1642", "CHEMBL1201585"] } }

This server integrates with the ChEMBL REST API for programmatic access to chemical data. For more information about ChEMBL:

- ChEMBL Website:https://www.ebi.ac.uk/chembl/
- API Documentation:https://chembl.gitbook.io/chembl-interface-documentation/web-services
- REST API Guide:https://www.ebi.ac.uk/chembl/api/data/docs

chembl-server/ ├── src/ │ └── index.ts # Main server implementation ├── build/ # Compiled JavaScript output ├── package.json # Node.js dependencies and scripts ├── tsconfig.json # TypeScript configuration └── README.md # This file

- @modelcontextprotocol/sdk: Core MCP SDK for server implementation
- axios: HTTP client for ChEMBL API requests
- typescript: TypeScript compiler for development
- Fork the repository
- Create a feature branch
- Make your changes
- Add tests if applicable
- Submit a pull request
- Check theChEMBL API documentation
- Review theModel Context Protocol specification
- Open an issue on the repository

This comprehensive ChEMBL MCP Server is developed byAugmented Nature, a leading innovator in AI-powered bioinformatics and computational chemistry solutions. Augmented Nature specializes in creating advanced tools that bridge the gap between artificial intelligence and chemical research, enabling researchers to unlock deeper insights from chemical and biological data.

author = {Moudather Chelbi}, title = {ChEMBL MCP Server}, year = {2025}, howpublished = {https://github.com/Augmented-Nature/ChEMBL-MCP-Server}, note = {Accessed: 2025-06-29}

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