Rosetta MCP

Protein modeling and design using the Rosetta suite via Docker

An MCP (Model Context Protocol) server for molecular modeling with 7 core tools:

• Protein structure refinement using Relax protocol

• Mutation stability analysis (ΔΔG calculations)

• Submit protein-protein docking jobs with async tracking

• Submit loop modeling jobs

• Submit protein-ligand docking jobs

• Monitor and retrieve job results

• List available example structures

Quick Start with Docker

Approach 1: Pull Pre-built Image from GitHub

The fastest way to get started. A pre-built Docker image is automatically published to GitHub Container Registry on every release.

# Pull the latest image
docker pull ghcr.io/macromnex/rosetta_mcp:latest

# Register with Claude Code (runs as current user to avoid permission issues)
claude mcp add rosetta -- docker run -i --rm --user `id -u`:`id -g` -v `pwd`:`pwd` ghcr.io/macromnex/rosetta_mcp:latest

Note: Run from your project directory. `pwd` expands to the current working directory.

Requirements:

• Docker

• Claude Code installed

That's it! The Rosetta MCP server is now available in Claude Code.

Approach 2: Build Docker Image Locally

Build the image yourself and install it into Claude Code. Useful for customization or offline environments.

# Clone the repository
git clone https://github.com/MacromNex/rosetta_mcp.git
cd rosetta_mcp

# Build the Docker image
docker build -t rosetta_mcp:latest .

# Register with Claude Code (runs as current user to avoid permission issues)
claude mcp add rosetta -- docker run -i --rm --user `id -u`:`id -g` -v `pwd`:`pwd` rosetta_mcp:latest

Note: Run from your project directory. `pwd` expands to the current working directory.

Requirements:

• Docker

• Claude Code installed

• Git (to clone the repository)

About the Docker Flags:

• -i — Interactive mode for Claude Code

• --rm — Automatically remove container after exit

• --user `id -u`:`id -g` — Runs the container as your current user, so output files are owned by you (not root)

• -v — Mounts your project directory so the container can access your data

Related MCP server: Structural Biology MCP Server

Verify Installation

After adding the MCP server, you can verify it's working:

# List registered MCP servers
claude mcp list

# You should see 'rosetta' in the output

In Claude Code, you can now use all 7 Rosetta tools:

• refine_protein_structure

• calculate_ddg

• submit_protein_docking

• submit_loop_modeling

• submit_ligand_docking

• get_job_status

• get_job_result

Next Steps

• Detailed documentation: See detail.md for comprehensive guides on:

  • Available MCP tools and parameters

  • Local Python environment setup (alternative to Docker)

  • Example workflows and use cases

  • PyRosetta license information

  • Troubleshooting

Usage Examples

Once registered, you can use the Rosetta tools directly in Claude Code. Here are some common workflows:

Example 1: Protein Structure Refinement

I have a protein structure at /path/to/protein.pdb. Can you use refine_protein_structure to refine it with 5 trajectories and 100 cycles, saving results to /path/to/results/?

Example 2: Mutation Stability Analysis

I want to analyze how mutations A10G, A10L, and A10F affect the stability of /path/to/protein.pdb. Can you use calculate_ddg with 5 trajectories and report which mutations are stabilizing vs destabilizing?

Example 3: Protein-Protein Docking

I have a protein complex at /path/to/complex.pdb with chain break at residue 150. Can you submit a docking job using submit_protein_docking with 20 trajectories, save results to /path/to/docking/, and monitor progress until completion?

Troubleshooting

Docker not found?

docker --version  # Install Docker if missing

Claude Code not found?

# Install Claude Code
npm install -g @anthropic-ai/claude-code

PyRosetta not available?

• All tools work in demo mode without PyRosetta

• For full functionality, a PyRosetta academic or commercial license is required

• See detail.md for PyRosetta installation instructions

License

Rosetta License — Based on Rosetta Commons software suite. Academic use is free with registration.