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.

- 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

# 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

# From source python -m mcp_server # If installed via pip pubchem-mcp

- Install Claude for Desktop
- 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" ] } } }

- Restart Claude for Desktop
- You can now use the PubChem tools in Claude

- "Find information about aspirin in PubChem"
- "What are the properties of compound CID 2244?"
- "Show me the structure of paracetamol"

- 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...

# 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

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