📌Overview

Purpose: Molecule-MCP aims to facilitate integration between molecular science tools and Claude AI, enhancing molecule modeling through collaborative efforts.

Overview: Molecule-MCP serves as a model-context-protocol server that connects various molecular science tools to Claude AI, enabling direct interaction and control of these tools. This collaborative framework allows Claude to act as a co-scientist in the molecular modeling process, promoting efficient and informed decision-making in scientific research.

Key Features:

Integration with Claude AI: Directly connects molecular science tools like PyMOL and ChimeraX to Claude AI, enhancing the modeling experience and allowing AI-assisted workflows.
Model Context Protocol (MCP): Utilizes MCP to enable seamless communication between Claude and the connected tools, streamlining operations and improving overall efficiency in molecular modeling tasks.

Molecule-MCP

Molecule-MCP is a model-context-protocol server for molecules. It connects molecule science-related tools to Claude AI through the Model Context Protocol (MCP), allowing Claude to directly interact with and control these tools and act as a co-scientist. This integration enables prompt-assisted molecule modeling.

Installation

⚠️ Note: Molecule-MCP requires Claude Desktop to be installed and running.

Go to Claude > Settings > Developer > Edit Config > claude_desktop_config.json to include the following configuration:

{
  "mcpServers": {
    "pymol": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/pymol_server.py"
      ]
    },
    "chimerax": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/ChimeraX_server.py"
      ]
    },
    "gromacs_copilot": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/mcp_server.py"
      ]
    }
  }
}

Install mcp and get the script:

pip install "mcp[cli]" chatmol
pip install git+https://github.com/ChatMol/gromacs_copilot.git  # optional, for running gromacs_copilot
which mcp

Copy the displayed path to mcp and replace /path/to/mcp in the configuration above with the actual path.

Clone the Molecule-MCP repository and get its path:

git clone https://github.com/ChatMol/molecule-mcp.git
cd molecule-mcp
pwd

Copy the displayed path and replace /path/to/molecule-mcp in the configuration above with the actual path.

Disclaimer

Molecule-MCP is provided "as is" without warranty of any kind, express or implied. The authors and contributors disclaim all warranties including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. Users employ this software at their own risk.

The authors bear no responsibility for any consequences arising from the use, misuse, or misinterpretation of this software or its outputs. Results obtained through Molecule-MCP should be independently validated prior to use in research, publications, or decision-making processes.

This software is intended for research and educational purposes only. Users are solely responsible for ensuring compliance with applicable laws, regulations, and ethical standards in their jurisdiction.