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SureChembl MCP Server

A comprehensive Model Context Protocol (MCP) server for accessing the SureChEMBL chemical patent database.

Installation

Add the following to your MCP client configuration file.

Configuration

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

You can access SureChEMBL’s chemical patent data through this MCP server, enabling patent search, chemical discovery, structure viewing, and patent analytics. Use it with an MCP client to run tools that query patents, fetch chemical data, visualize structures, and export results for analysis.

How to use

To use this MCP server, start the server locally and connect your MCP client to it. You will interact with a set of tools that let you search patents, retrieve documents, find chemicals by name or structure, generate images, export data, and run advanced analyses. Each tool is invoked by your client with a specific tool name and a set of arguments.

How to install

Prerequisites are installed on your system before you begin.

# Ensure you have Node.js 18+ installed on your system
# Then obtain the MCP server files and place them in a working directory

# Install dependencies
npm install

# Build the server (transpiles TypeScript to JavaScript)
npm run build

# Start the server (production/run mode)
npm start

# Optional development workflow
# Watch for changes and recompile automatically
npm run watch

Additional configuration and usage notes

If you want to run the server from your workstation and connect via an MCP client, you can define a local stdio MCP configuration that points to the built entry point.

Resource examples

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

Usage notes for MCP clients

Your MCP client will send a request to the server specifying the tool name and arguments. The server responds with the data, errors if any, and structured results. Use the available tools to perform document and patent searches, chemical lookups, structure visualizations, data exports, and advanced analyses.

Available tools

search_patents

Search patents by text, keywords, or identifiers with support for limits and offsets.

get_document_content

Retrieve complete patent documents with chemical annotations.

get_patent_family

Fetch patent family members and relationships for a given patent.

search_by_patent_number

Search patents by a specific patent or publication number.

search_chemicals_by_name

Find chemicals by name or synonym.

get_chemical_by_id

Get detailed information for a chemical by its SureChEMBL ID.

search_by_smiles

Search chemicals using a SMILES string.

search_by_inchi

Search chemicals by InChI or InChIKey.

get_chemical_image

Generate a visual image of a chemical structure from SMILES or notation.

get_chemical_properties

Retrieve molecular properties and descriptors for a chemical.

export_chemicals

Bulk export chemical data in CSV or XML format.

analyze_patent_chemistry

Analyze chemical content and annotations within a patent document.

get_chemical_frequency

Return frequency statistics of a chemical across the patent database.

search_similar_structures

Find structurally similar chemicals using a similarity search.

get_patent_statistics

Provide statistics about chemical content in a patent document.