ChemBL-MCP

April 17, 2025 ยท View on GitHub

An MCP (Model Context Protocol) server for accessing ChEMBL data. This server provides tools for querying the ChEMBL database for molecules, targets, assays, activities, and documents.

Features

  • Search for molecules by name, structure, or similarity
  • Retrieve detailed information about molecules, targets, and assays
  • Access bioactivity data and related documents
  • Compatible with any MCP client, including Claude for Desktop

Installation

Option 1: From GitHub

# Clone the repository
git clone https://github.com/BioContext/ChemBL-MCP.git
cd ChemBL-MCP

# Create a virtual environment
uv venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate

# Install dependencies
pip install -r requirements.txt

Option 2: Using pip (Once published)

pip install chembl-mcp

Usage

Running as a standalone server

# From source
python -m mcp_server

# If installed via pip
chembl-mcp

Using with Claude for Desktop

  1. Install Claude for Desktop
  2. Configure Claude for Desktop to use this server by editing ~/Library/Application Support/Claude/claude_desktop_config.json (macOS/Linux) or %AppData%\Claude\claude_desktop_config.json (Windows):
{
    "mcpServers": {
        "chembl": {
            "command": "python",
            "args": [
                "-m",
                "mcp_server"
            ]
        }
    }
}
  1. Restart Claude for Desktop
  2. You can now use the ChEMBL tools in Claude

Example queries for Claude

  • "Find information about aspirin in ChEMBL"
  • "What are the targets of propranolol?"
  • "Show me bioactivity data for compound CHEMBL25"

Available Tools

  • search_molecule: Search for molecules by name or structure
  • get_molecule_details: Get detailed information about a molecule
  • get_similar_molecules: Find molecules similar to a given one
  • search_targets: Search for biological targets
  • get_target_details: Get detailed information about a target
  • search_assays: Search for assays
  • get_bioactivities: Get bioactivity data for a molecule
  • And more...

Development

# Clone the repository
git clone https://github.com/BioContext/ChemBL-MCP.git
cd ChemBL-MCP

# Create a virtual environment
uv venv
source .venv/bin/activate

# Install development dependencies
pip install -e ".[dev]"

# Run tests
pytest

License

MIT License