# 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
```bash
# 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)
```bash
pip install pubchem-mcp
```
## Usage
### Running as a standalone server
```bash
# 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):
```json
{
"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
```bash
# 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
