PubChem-MCP

Access PubChem's database for chemical compounds, substances, and bioassays.

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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: .venv\Scripts\activate

# 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%\Claude\claude_desktop_config.json (Windows):
{
    "mcpServers": {
        "pubchem": {
            "command": "python",
            "args": [
                "-m",
                "mcp_server"
            ]
        }
    }
}
  1. Restart Claude for Desktop
  2. 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: .venv\Scripts\activate

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

# Run tests
pytest

License

MIT License

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