SureChEMBL-MCP-Server

Name: SureChEMBL-MCP-Server
Availability: InStock
Author: Augmented-Nature

SureChEMBL-MCP-Serverは、化学データの収集と解析を行うためのサーバーです。特に、化学物質の情報を効率的に取得し、データベースに格納する機能を持っています。ユーザーはAPIを通じてデータにアクセスし、さまざまな分析を実施することができます。

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README

Unofficial SureChEMBL MCP Server

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

Developed by Augmented Nature

Overview

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:

Patent Intelligence: Search and analyze chemical patents
Chemical Discovery: Find compounds and their patent coverage
Prior Art Research: Identify existing chemical disclosures
Competitive Analysis: Track chemical developments by companies
Structure-Activity Analysis: Correlate chemical structures with patent claims

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

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

API Examples

Search for Chemicals by Name

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

Get Patent Document Content

// Get full patent document with chemical annotations
await use_mcp_tool({
  server_name: "surechembl-server",
  tool_name: "get_document_content",
  arguments: {
    document_id: "WO-2020096695-A1",
  },
});

Generate Chemical Structure Image

// Generate structure image from SMILES
await use_mcp_tool({
  server_name: "surechembl-server",
  tool_name: "get_chemical_image",
  arguments: {
    structure: "CC(=O)OC1=CC=CC=C1C(=O)O",
    width: 300,
    height: 200,
  },
});

Analyze Patent Chemistry

// 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",
  },
});

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.

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

Fork the repository
Create a feature branch
Make your changes
Add tests if applicable
Submit a pull request

License

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:

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

**SureChEMBL MCP Server** - Empowering chemical patent intelligence through the Model Context Protocol.

作者情報

Augmented-Nature

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bioinformatics cheminformatics intellectual-property mcp-server model-context-protocol patents surechembl