Surechembl MCP Server

🚀 Unofficial SureChEMBL MCP Server

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

Developed by Augmented Nature

🚀 Quick Start

SureChEMBL is a large - scale chemical patent database that provides access to chemical structures and their associated patent documents. This MCP server enables seamless integration with SureChEMBL's API, offering powerful tools for various chemical and patent - related tasks.

✨ 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

• search_patents: Search patents by text, keywords, or identifiers.
  • Parameters:
    • query (string, required): Search query
    • limit (number, optional): Results limit (1 - 1000, default: 25)
    • offset (number, optional): Results offset (default: 0)
• get_document_content: Get complete patent document content with chemical annotations.
  • Parameters:
    • document_id (string, required): Patent document ID (e.g., WO - 2020096695 - A1)
• get_patent_family: Get patent family members and relationships.
  • Parameters:
    • patent_id (string, required): Patent ID to find family members for
• search_by_patent_number: Search for patents by specific patent numbers.
  • Parameters:
    • patent_number (string, required): Patent or publication number

Chemical Search & Retrieval

• search_chemicals_by_name: Search for chemicals by name, synonym, or common name.
  • Parameters:
    • name (string, required): Chemical name or synonym
    • limit (number, optional): Results limit (1 - 1000, default: 25)
• get_chemical_by_id: Get detailed chemical information by SureChEMBL chemical ID.
  • Parameters:
    • chemical_id (string, required): SureChEMBL chemical ID (numeric)
• search_by_smiles: Search for chemicals by SMILES structure notation.
  • Parameters:
    • smiles (string, required): SMILES string
    • limit (number, optional): Results limit (1 - 1000, default: 25)
• search_by_inchi: Search for chemicals by InChI or InChI key.
  • Parameters:
    • inchi (string, required): InChI string or InChI key
    • limit (number, optional): Results limit (1 - 1000, default: 25)

Structure & Visualization

• get_chemical_image: Generate chemical structure image from SMILES or other structure notation.
  • Parameters:
    • structure (string, required): SMILES string or structure notation
    • height (number, optional): Image height in pixels (default: 200)
    • width (number, optional): Image width in pixels (default: 200)
• get_chemical_properties: Get molecular properties and descriptors for a chemical.
  • Parameters:
    • chemical_id (string, required): SureChEMBL chemical ID

Data Export & Analysis

• export_chemicals: Bulk export chemical data in CSV or XML format.
  • Parameters:
    • chemical_ids (array, required): Array of SureChEMBL chemical IDs (1 - 100)
    • output_type (string, optional): Export format - 'csv' or 'xml' (default: csv)
    • kind (string, optional): ID type - 'cid' or 'smiles' (default: cid)
• analyze_patent_chemistry: Analyze chemical content and annotations in a patent document.
  • Parameters:
    • document_id (string, required): Patent document ID to analyze

Advanced Analysis Tools

• get_chemical_frequency: Get frequency statistics for chemicals across the patent database.
  • Parameters:
    • chemical_id (string, required): SureChEMBL chemical ID
• search_similar_structures: Find structurally similar chemicals using similarity search.
  • Parameters:
    • reference_id (string, required): Reference chemical ID for similarity search
    • threshold (number, optional): Similarity threshold (0.0 - 1.0, default: 0.7)
    • limit (number, optional): Number of results to return (1 - 100, default: 25)
• get_patent_statistics: Get statistical overview of chemical content in patents.
  • Parameters:
    • document_id (string, required): Patent document ID for statistics
    • include_annotations (boolean, optional): Include detailed annotation statistics (default: true)

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

MIT License - see LICENSE file for details.

Support

For issues and questions:

• GitHub Issues: [Report bugs and feature requests](https://github.com/augmented - nature/surechembl - mcp - server/issues)
• Documentation: SureChEMBL API Documentation

Related Projects

• [ChEMBL MCP Server](https://github.com/augmented - nature/chembl - mcp - server) - ChEMBL bioactivity database
• [PubChem MCP Server](https://github.com/augmented - nature/pubchem - mcp - server) - PubChem chemical database
• [UniProt MCP Server](https://github.com/augmented - nature/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}