Surechembl MCP Server

🚀 Unofficial SureChEMBL MCP Server

A comprehensive Model Context Protocol (MCP) server for accessing the SureChEMBL chemical patent database, providing tools for patent search, chemical discovery, structure analysis, and patent intelligence research.

Developed by Augmented Nature

🚀 Quick Start

The Unofficial SureChEMBL MCP Server is a powerful tool for accessing the SureChEMBL chemical patent database. It offers a wide range of functions to help you search, analyze, and visualize chemical patent information.

✨ Features

🔍 Document & Patent Search (4 tools)

• search_patents: Search patents by text, keywords, or identifiers.
• get_document_content: Get complete patent document content with chemical annotations.
• get_patent_family: Get patent family members and relationships.
• search_by_patent_number: Search by specific patent numbers.

🧪 Chemical Search & Retrieval (4 tools)

• search_chemicals_by_name: Search chemicals by name or synonym.
• get_chemical_by_id: Get detailed chemical information by SureChEMBL ID.
• search_by_smiles: Search chemicals by SMILES structure notation.
• search_by_inchi: Search chemicals by InChI/InChI key.

🖼️ Structure & Visualization (2 tools)

• get_chemical_image: Generate chemical structure images.
• get_chemical_properties: Get molecular properties and descriptors.

📊 Data Export & Analysis (2 tools)

• export_chemicals: Bulk export chemical data (CSV/XML).
• analyze_patent_chemistry: Analyze chemical content in patents.

🔬 Advanced Analysis Tools (3 tools)

• get_chemical_frequency: Get frequency statistics for chemicals across patent database.
• search_similar_structures: Find structurally similar chemicals using similarity search.
• get_patent_statistics: Get statistical overview of chemical content in patents.

📚 Resource Templates

• surechembl://document/{doc_id}: Patent document content.
• surechembl://chemical/{chem_id}: Chemical compound data.
• surechembl://family/{patent_id}: Patent family information.
• surechembl://search/{query}: Search results.

📦 Installation

Prerequisites

• Node.js 18+
• npm or yarn

Install Dependencies

npm install

Build the Server

npm run build

Development Mode

npm run watch

💻 Usage Examples

Running the Server

npm start

Using with Claude Desktop

Add to your Claude Desktop configuration file:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%/Claude/claude_desktop_config.json

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

Using with MCP Inspector

npm run inspector

Basic Usage

// Search for aspirin-related compounds
await use_mcp_tool({
  server_name: "surechembl-server",
  tool_name: "search_chemicals_by_name",
  arguments: {
    name: "aspirin",
    limit: 10,
  },
});

Advanced Usage

// Analyze chemical annotations in a patent
await use_mcp_tool({
  server_name: "surechembl-server",
  tool_name: "analyze_patent_chemistry",
  arguments: {
    document_id: "US-2021123456-A1",
  },
});

📚 Documentation

Tool Reference

Document & Patent Search

Chemical Search & Retrieval

Structure & Visualization

Data Export & Analysis

Advanced Analysis Tools

Resource Templates

Document Resource

surechembl://document/{doc_id}

Access complete patent document content with chemical annotations.

Chemical Resource

surechembl://chemical/{chem_id}

Access chemical compound information and properties.

Patent Family Resource

surechembl://family/{patent_id}

Access patent family members and relationships.

Search Resource

surechembl://search/{query}

Access chemical search results for a query.

🔧 Technical Details

Error Handling

The server includes comprehensive error handling for:

• Invalid API parameters
• Network timeouts and connection issues
• API rate limiting
• Malformed chemical structures
• Missing documents or chemicals

All errors are returned with descriptive messages and appropriate error codes.

Rate Limiting

The server respects SureChEMBL's API rate limits:

• 30 - second timeout for complex requests
• Respectful request spacing
• Automatic retry logic for transient failures

Development

Project Structure

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

Available Scripts

• npm run build: Compile TypeScript to JavaScript.
• npm run watch: Watch mode for development.
• npm run inspector: Run MCP inspector.
• npm start: Start the server.
• npm run dev: Development mode with watch.

Contributing

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

📄 License

This project is under the MIT License - see LICENSE file for details.

Support

For issues and questions:

• GitHub Issues: Report bugs and feature requests
• Documentation: SureChEMBL API Documentation

Related Projects

• ChEMBL MCP Server - ChEMBL bioactivity database
• PubChem MCP Server - PubChem chemical database
• UniProt MCP Server - UniProt protein database

Citation

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

@misc{surechemblmcp2025, 
author = {Moudather Chelbi},
title = {SureChEMBL MCP Server},
year = {2025},
howpublished = {https://github.com/Augmented-Nature/SureChEMBL-MCP-Server},
note = {Accessed: 2025-06-29}
}