Molecule-MCP

Molecule-MCP is a model-context-protocol server designed for molecular science, enabling Claude AI to interact with molecule-related tools as a co-scientist through the Model Context Protocol (MCP). This integration facilitates prompt-assisted molecule modeling.

Installation

Note: Molecule-MCP requires Claude Desktop.

1. Configure Claude by editing claude_desktop_config.json to include MCP server configurations for "pymol" and "chimerax," specifying the command as the path to mcp and arguments to run the respective server scripts (pymol_server.py, chimerax_server.py).
2. Install mcp and chatmol using pip install mcp chatmol. Locate the mcp executable using which mcp and update the Claude configuration with its path. Clone the repository using git clone https://github.com/ChatMol/molecule-mcp.git, navigate into it, and use pwd to get the path to the cloned directory, then update the Claude configuration with this path.

Disclaimer

Molecule-MCP is provided "as is" without warranty. Users assume all risks. Validate results independently. Intended for research and educational purposes only. Users are responsible for compliance with laws and ethical standards.