Provides configuration support for running the SureChEMBL MCP server with Claude Desktop on macOS systems.
Enables running the SureChEMBL MCP server which provides tools for accessing the SureChEMBL chemical patent database for patent searches, chemical discovery, and structure analysis.
Used for implementing the SureChEMBL MCP server with type-safe API interactions to the SureChEMBL chemical patent database.
Supported as an export format for chemical data from the SureChEMBL database.
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 identifiersget_document_content
- Get complete patent document content with chemical annotationsget_patent_family
- Get patent family members and relationshipssearch_by_patent_number
- Search by specific patent numbers
🧪 Chemical Search & Retrieval (4 tools)
search_chemicals_by_name
- Search chemicals by name or synonymget_chemical_by_id
- Get detailed chemical information by SureChEMBL IDsearch_by_smiles
- Search chemicals by SMILES structure notationsearch_by_inchi
- Search chemicals by InChI/InChI key
🖼️ Structure & Visualization (2 tools)
get_chemical_image
- Generate chemical structure imagesget_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 databasesearch_similar_structures
- Find structurally similar chemicals using similarity searchget_patent_statistics
- Get statistical overview of chemical content in patents
📚 Resource Templates
surechembl://document/{doc_id}
- Patent document contentsurechembl://chemical/{chem_id}
- Chemical compound datasurechembl://family/{patent_id}
- Patent family informationsurechembl://search/{query}
- Search results
Installation
Prerequisites
- Node.js 18+
- npm or yarn
Install Dependencies
Build the Server
Development Mode
Usage
Running the Server
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
Using with MCP Inspector
API Examples
Search for Chemicals by Name
Get Patent Document Content
Generate Chemical Structure Image
Analyze Patent Chemistry
Tool Reference
Document & Patent Search
search_patents
Search patents by text, keywords, or identifiers.
Parameters:
query
(string, required): Search querylimit
(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 synonymlimit
(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 stringlimit
(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 keylimit
(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 notationheight
(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 searchthreshold
(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 statisticsinclude_annotations
(boolean, optional): Include detailed annotation statistics (default: true)
Resource Templates
Document Resource
Access complete patent document content with chemical annotations.
Chemical Resource
Access chemical compound information and properties.
Patent Family Resource
Access patent family members and relationships.
Search Resource
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
Available Scripts
npm run build
- Compile TypeScript to JavaScriptnpm run watch
- Watch mode for developmentnpm run inspector
- Run MCP inspectornpm start
- Start the servernpm 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:
This server cannot be installed
A comprehensive Model Context Protocol (MCP) server for accessing the SureChEMBL chemical patent database.
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