Chembl MCP Server

🚀 Unofficial ChEMBL MCP Server

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

Developed by Augmented Nature

✨ Features

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.

Bioactivity & Assay Data (5 tools)

• 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.

Chemical Property Analysis (4 tools)

• 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.

Resource Templates

• Direct access to ChEMBL data via URI templates for seamless integration.

📦 Installation

Prerequisites

• Node.js (v16 or higher)
• npm or yarn

Setup

1. Clone the repository:

git clone <repository-url>
cd chembl-server

2. Install dependencies:

npm install

3. Build the project:

npm run build

🐳 Docker

Building the Docker Image

Build the Docker image:

docker build -t chembl-mcp-server .

Running with Docker

Run the container:

docker run -i chembl-mcp-server

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

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

💻 Usage

As an MCP Server

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

npm start

Adding to MCP Client Configuration

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": {}
    }
  }
}

🛠️ Available Tools

1. search_compounds

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

Parameters:

• 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).

Example:

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

2. get_compound_info

Get detailed information for a specific compound by ChEMBL ID.

Parameters:

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

Example:

{
  "chembl_id": "CHEMBL25"
}

3. search_targets

Search for biological targets by name or type.

Parameters:

• 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).

Example:

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

4. search_activities

Search bioactivity measurements and assay results.

Parameters:

• 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).

Example:

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

5. batch_compound_lookup

Process multiple ChEMBL IDs efficiently.

Parameters:

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

Example:

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

🌐 Resource Templates

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

1. Compound Information

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

2. Target Information

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

3. Assay Information

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

4. Activity Information

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

5. Search Results

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

💡 Examples

Basic Compound Search

Search for aspirin-related compounds:

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

Get Detailed Compound Information

Retrieve comprehensive information about aspirin:

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

Target-based Search

Find compounds tested against dopamine receptors:

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

Bioactivity Analysis

Search for IC50 data against a specific target:

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

Batch Processing

Process multiple compounds efficiently:

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

🔌 API Integration

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

All API requests include:

• User-Agent: ChEMBL-MCP-Server/1.0.0
• Timeout: 30 seconds
• Base URL: https://www.ebi.ac.uk/chembl/api/data

⚠️ Error Handling

The server includes comprehensive error handling:

• Input Validation: All parameters are validated using type guards.
• API Errors: Network and API errors are caught and returned with descriptive messages.
• Timeout Handling: Requests timeout after 30 seconds.
• Graceful Degradation: Partial failures are handled appropriately.

🛠️ Development

Build the Project

npm run build

Development Mode

Run TypeScript compiler in watch mode:

npm run dev

Project Structure

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

📦 Dependencies

• @modelcontextprotocol/sdk: Core MCP SDK for server implementation.
• axios: HTTP client for ChEMBL API requests.
• typescript: TypeScript compiler for development.

📄 License

MIT License

🤝 Contributing

1. Fork the repository.
2. Create a feature branch.
3. Make your changes.
4. Add tests if applicable.
5. Submit a pull request.

🆘 Support

For issues and questions:

1. Check the ChEMBL API documentation.
2. Review the Model Context Protocol specification.
3. Open an issue on the repository.

👨‍🔬 About Augmented Nature

This comprehensive ChEMBL MCP Server is developed by Augmented 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.

📖 Complete Tool Reference

Core Chemical Search & Retrieval Tools

1. search_compounds - Search ChEMBL database by name, synonym, or identifier.
2. get_compound_info - Get detailed compound information by ChEMBL ID.
3. search_by_inchi - Find compounds by InChI key or InChI string.
4. get_compound_structure - Retrieve chemical structures in various formats.
5. search_similar_compounds - Find chemically similar compounds using Tanimoto similarity.

Target Analysis & Drug Discovery Tools

6. search_targets - Search for biological targets by name or type.
7. get_target_info - Get detailed target information by ChEMBL target ID.
8. get_target_compounds - Get compounds tested against specific targets.
9. search_by_uniprot - Find ChEMBL targets by UniProt accession.
10. get_target_pathways - Get biological pathways associated with targets.

Bioactivity & Assay Data Tools

11. search_activities - Search bioactivity measurements and assay results.
12. get_assay_info - Get detailed assay information by ChEMBL assay ID.
13. search_by_activity_type - Find bioactivity data by activity type and value range.
14. get_dose_response - Get dose-response data and activity profiles.
15. compare_activities - Compare bioactivity data across multiple compounds.

Drug Development & Clinical Data Tools

16. search_drugs - Search for approved drugs and clinical candidates.
17. get_drug_info - Get drug development status and clinical trial information.
18. search_drug_indications - Search for therapeutic indications and disease areas.
19. get_mechanism_of_action - Get mechanism of action and target interaction data.

Chemical Property Analysis Tools

20. analyze_admet_properties - Analyze ADMET properties.
21. calculate_descriptors - Calculate molecular descriptors and physicochemical properties.
22. predict_solubility - Predict aqueous solubility and permeability properties.
23. assess_drug_likeness - Assess drug-likeness using Lipinski Rule of Five.

Advanced Search & Cross-Reference Tools

24. substructure_search - Find compounds containing specific substructures.
25. batch_compound_lookup - Process multiple ChEMBL IDs efficiently.
26. get_external_references - Get links to external databases.
27. advanced_search - Complex queries with multiple chemical and biological filters.

📜 Changelog

v1.0.0 - Initial Release

• Comprehensive Chemical Intelligence: 27 specialized tools for drug discovery.
• Core Functionality: Compound search, target analysis, bioactivity data.
• Advanced Features: Similarity search, batch processing, cross-references.
• Resource Templates: Direct URI-based access to ChEMBL data.
• Docker Support: Containerized deployment with security best practices.
• Professional Documentation: Complete tool reference and examples.
• Developed by Augmented Nature: Professional chemical informatics platform.

📚 Citation

If you use this project in your research or publications, please cite it as follows:

@misc{chemblmcp2025, 
author = {Moudather Chelbi},
title = {ChEMBL MCP Server},
year = {2025},
howpublished = {https://github.com/Augmented-Nature/ChEMBL-MCP-Server},
note = {Accessed: 2025-06-29}
}