PubChem-MCP

An MCP (Model Context Protocol) server for accessing PubChem data. This server provides tools for querying the PubChem database for compounds, substances, bioassays, and related information.

Features

• Search for compounds by name, structure, or identifier
• Retrieve detailed information about compounds and substances
• Access bioassay data and molecular properties
• Query chemical classifications and cross-references
• Compatible with any MCP client, including Claude for Desktop

Installation

Option 1: From GitHub

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

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

# Install dependencies
pip install -r requirements.txt

Option 2: Using pip (Once published)

pip install pubchem-mcp

Usage

Running as a standalone server

# From source
python -m mcp_server

# If installed via pip
pubchem-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%Claudeclaude_desktop_config.json (Windows):

{
    "mcpServers": {
        "pubchem": {
            "command": "python",
            "args": [
                "-m",
                "mcp_server"
            ]
        }
    }
}

3. Restart Claude for Desktop
4. You can now use the PubChem tools in Claude

Example queries for Claude

• “Find information about aspirin in PubChem”
• “What are the properties of compound CID 2244?”
• “Show me the structure of paracetamol”

Available Tools

• search_compound: Search for compounds by name or identifier
• get_compound_details: Get detailed information about a compound
• get_compound_properties: Get physical and chemical properties of a compound
• search_bioassay: Search for bioassays
• get_substance_details: Get detailed information about a substance
• And more…

Development

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

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

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

# Run tests
pytest

License

MIT License