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
- 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
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 identifierget_compound_details: Get detailed information about a compoundget_compound_properties: Get physical and chemical properties of a compoundsearch_bioassay: Search for bioassaysget_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