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Molecule Server

v1.0.0•Data Science & ML•stable

A model-context-protocol server for molecules.

moleculemcpai-integration
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What is Molecule Server?

Molecule Server is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to model-context-protocol server for molecules.

A model-context-protocol server for molecules.

This server falls under the Data Science & ML category on MCPgee, the world's largest MCP server directory with 33,000+ servers.

Features

  • A model-context-protocol server for molecules.

Use Cases

Work with molecular structures and chemical data.
Query molecule properties and relationships.
Support cheminformatics analysis through MCP.
ChatMol

Maintainer

LicenseMIT
Languagepython
Versionv1.0.0
UpdatedApr 23, 2026
Statushealthy
Maintenanceactive

Works with

ClaudeOpenAIwindowsmacoslinux
View SourceBrowse All Servers

Installation

Manual Installation

npx molecule

Configuration

Configuration Details

Config File

claude_desktop_config.json

Performance

Response Metrics

Response Time< 200ms
ThroughputMedium

Resource Usage

Memory UsageLow
CPU UsageLow

How to Set Up and Use Molecule Server

Molecule MCP Server is a Python-based Model Context Protocol server that connects AI assistants to molecular visualization and simulation software — specifically PyMOL, UCSF ChimeraX, and GROMACS. It enables Claude to directly control these tools for molecular structure visualization, structural analysis, and molecular dynamics simulations, acting as a computational collaborator for cheminformatics and structural biology research. Scientists use it to automate repetitive structure analysis workflows and explore molecular properties through natural language.

Prerequisites

  • Python 3.9+ installed on your system
  • Claude Desktop installed and running
  • PyMOL installed (open-source or commercial) for molecular visualization
  • UCSF ChimeraX installed for structural analysis and modeling
  • GROMACS installed (optional) for molecular dynamics simulations
1

Install the mcp CLI and chatmol package

Install the MCP CLI tool and the chatmol Python package, which provides the core molecule handling functionality.

pip install "mcp[cli]" chatmol
2

Install GROMACS Copilot (optional)

For molecular dynamics simulation support, install the GROMACS Copilot package from GitHub.

pip install git+https://github.com/ChatMol/gromacs_copilot.git
3

Find the mcp binary path

Locate the full path to the mcp binary — you will need it in the Claude Desktop configuration.

which mcp
4

Clone the molecule-mcp repository

Clone the repository to get the server script files for PyMOL, ChimeraX, and GROMACS.

git clone https://github.com/ChatMol/molecule-mcp.git
cd molecule-mcp && pwd
5

Configure Claude Desktop

Open Claude Desktop Settings → Developer and edit claude_desktop_config.json to register the three MCP servers. Replace /path/to/mcp with the output of 'which mcp' and /path/to/molecule-mcp with the cloned repo path.

{
  "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/gromacs_server.py"]
    }
  }
}

Molecule Server Examples

Client configuration

Full Claude Desktop configuration for all three molecule servers. Run 'which mcp' and 'pwd' in the molecule-mcp directory to fill in the correct paths.

{
  "mcpServers": {
    "pymol": {
      "command": "/usr/local/bin/mcp",
      "args": ["run", "/home/user/molecule-mcp/pymol_server.py"]
    },
    "chimerax": {
      "command": "/usr/local/bin/mcp",
      "args": ["run", "/home/user/molecule-mcp/chimerax_server.py"]
    },
    "gromacs_copilot": {
      "command": "/usr/local/bin/mcp",
      "args": ["run", "/home/user/molecule-mcp/gromacs_server.py"]
    }
  }
}

Prompts to try

Use natural language to drive molecular visualization and simulation workflows.

- "Open the PDB structure 1ABC in PyMOL and render it as a cartoon with ligands shown as sticks"
- "In ChimeraX, calculate the surface area of the active site residues in the loaded structure"
- "Load the GROMACS trajectory file and analyze the RMSD of the protein backbone over time"
- "Color the protein by secondary structure in PyMOL and save a high-resolution image"
- "Find all residues within 5 angstroms of the ligand and highlight them in ChimeraX"

Troubleshooting Molecule Server

mcp binary not found after pip install

The mcp binary may not be in your PATH. Run 'pip show mcp' to find the install location, then check the bin directory (e.g., ~/.local/bin/mcp). Add that directory to your PATH or use the full absolute path in claude_desktop_config.json.

PyMOL or ChimeraX server fails to start

Ensure PyMOL or ChimeraX is installed and accessible from the command line. The server scripts expect these applications to be installed in their default locations. Check the Claude Desktop logs (Help → Open Logs Folder) for the specific error message.

Research results differ from expected molecular data

The README explicitly notes this is research-only software without warranties. Always independently validate results (structure coordinates, energy values, simulation outputs) before using them in publications or critical decisions.

Frequently Asked Questions about Molecule Server

What is Molecule Server?

Molecule Server is a Model Context Protocol (MCP) server that model-context-protocol server for molecules. It connects AI assistants to external tools and data sources through a standardized interface.

How do I install Molecule Server?

Follow the installation instructions on the Molecule Server GitHub repository. Clone the repo, install dependencies, and add the server config to your AI client.

Which AI clients work with Molecule Server?

Molecule Server works with all major MCP-compatible AI clients including Claude Desktop, Claude Code, Cursor, VS Code (GitHub Copilot), Windsurf, and Cline.

Is Molecule Server free to use?

Yes, Molecule Server is open source and available under the MIT license. You can use it freely in both personal and commercial projects.

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Quick Config Preview

{ "mcpServers": { "molecule": { "command": "npx", "args": ["-y", "molecule"] } } }

Add this to your claude_desktop_config.json or .cursor/mcp.json

Read the full setup guide →

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