ChemBL-MCP

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"
            ]
        }
    }
}

3. Restart Claude for Desktop
4. 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