PubChem MCP Server
About
Enables large language models to correctly query molecular databases and generate structure files
Explore
- Query compounds by name or PubChem CID
- Retrieve comprehensive compound data including:
- IUPAC name
- Molecular formula
- Molecular weight
- SMILES notation
- InChI and InChIKey
- Support for multiple output formats:
- JSON (default)
- CSV
- XYZ (3D structure)
- Built-in caching system to improve performance
- Automatic retry mechanism for API reliability
- Fallback 3D structure generation if PubChem 3D is unavailable
- Python 3.8+
- Requests library
- RDKit (optional, for enhanced 3D structure handling)
pip install -e .
pip install -e ".[rdkit]"
To use the server with Claude or other MCP-capable AI models, add the following to your MCP configuration file:
{
"mcpServers": {
"pubchem": {
"command": "python3",
"args": ["/path/to/pubchem-mcp-server/python_version/mcp_server.py"],
"env": {
"PYTHONUNBUFFERED": "1"
},
"disabled": false,
"autoApprove": [
"get_pubchem_data",
"download_structure"
]
}
}
}
```
A Model Context Protocol (MCP) server for retrieving chemical compound data from PubChem database.
Overview
PubChem MCP Server is a Python implementation of an MCP server that allows AI models to query chemical compound information from the PubChem database. It provides easy access to compound properties, 2D structures, and 3D molecular coordinates through a standard MCP interface.
Features
- Query compounds by name or PubChem CID
- Retrieve comprehensive compound data including:
- IUPAC name
- Molecular formula
- Molecular weight
- SMILES notation
- InChI and InChIKey
- Support for multiple output formats:
- JSON (default)
- CSV
- XYZ (3D structure)
- Built-in caching system to improve performance
- Automatic retry mechanism for API reliability
- Fallback 3D structure generation if PubChem 3D is unavailable
Requirements
- Python 3.8+
- Requests library
- RDKit (optional, for enhanced 3D structure handling)
Installation
From Source
```bash
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