Rosetta MCP Server

An MCP server that gives Claude working knowledge of the Rosetta protein-modeling stack: it runs and validates RosettaScripts XML, scores structures with PyRosetta, and translates protocols between Rosetta, PyRosetta and Biotite.


Type	MCP server
Supplier	Ariel Ben-Sasson (community OSS)
Availability	GA — npm `rosetta-mcp-server` 1.3.1; last upstream push 2026-04-05; written up by RosettaCommons 2025-10-20
Pricing	Free / OSS — MIT per the npm package manifest (Unverified — no `LICENSE` file is committed to the GitHub repo, so redistribution terms are declared only in `package.json`). Rosetta and PyRosetta themselves require a separate licence from the University of Washington (free for non-commercial academic use).
Capabilities	Read/Write — reads and writes structure/XML files, executes local Rosetta and PyRosetta runs
Verified	works · 2026-08-06 — install/launch commands confirmed against the upstream README
Security	caution · 2026-08-06 — no LICENSE file committed, MIT asserted only in prose; Rosetta/PyRosetta need their own academic license

How to install

The server is a Node wrapper around a Python process, so both runtimes are needed: Node 14+ and Python 3.8+.

Install the server:
```
npm install -g rosetta-mcp-server
```
Create the Python environment it drives, and install PyRosetta into it:
```
uv venv ~/.venvs/rosetta-mcp
~/.venvs/rosetta-mcp/bin/pip install pyrosetta-installer biotite
~/.venvs/rosetta-mcp/bin/python -c "import pyrosetta_installer as I; I.install_pyrosetta()"
```
(If you skip this, the PyRosetta-backed tools report “not available”; the server also exposes install_pyrosetta_installer to do it on first use.)
Claude Code — register it as a stdio server, passing the two paths it needs:
```
claude mcp add --transport stdio rosetta \
  --env PYTHON_BIN=$HOME/.venvs/rosetta-mcp/bin/python \
  --env ROSETTA_BIN=/path/to/rosetta_scripts.default.macosclangrelease \
  -- rosetta-mcp-server
```
Replace /path/to/rosetta_scripts.default.macosclangrelease with the absolute path to your compiled rosetta_scripts executable — the binary name encodes your platform and build (e.g. rosetta_scripts.default.linuxgccrelease on Linux), and it lives under <rosetta>/source/bin/. Omit ROSETTA_BIN if you only want the documentation, translation, validation and PyRosetta-scoring tools; run_rosetta_scripts and find_rosetta_scripts need it.

Claude Desktop — add the equivalent stdio entry to claude_desktop_config.json:

{
  "mcpServers": {
    "rosetta": {
      "command": "rosetta-mcp-server",
      "args": [],
      "env": {
        "PYTHON_BIN": "/Users/you/.venvs/rosetta-mcp/bin/python",
        "ROSETTA_BIN": "/path/to/rosetta_scripts.default.macosclangrelease"
      }
    }
  }
}

Use absolute paths here — Claude Desktop does not expand $HOME or ~.

You do not need to start the server yourself: Claude Code and Claude Desktop launch it over stdio. (The repo also ships rosetta_mcp_http.js for an HTTP deployment; that path is Unverified — the README documents only the stdio wrapper.)

What it does

18 tools, grouped by what they are for:

Documentation and discovery — get_rosetta_info, get_rosetta_help (accepts a mover name like FastRelax, a concept like constraints or docking, or a score function like ref2015, fetching live docs from rosettacommons.org), pyrosetta_introspect, search_rosetta_web_docs, get_rosetta_web_doc, get_cached_docs.
Execution and scoring — run_rosetta_scripts (runs a RosettaScripts XML protocol), pyrosetta_score (total or per_residue energy breakdown).
Translation — xml_to_pyrosetta, rosetta_to_biotite and biotite_to_rosetta (paired lookups across ~21 mappings covering structure I/O, SASA, RMSD, superimposition, secondary structure, contacts, hydrogen bonds, B-factors and angles), translate_rosetta_script_to_biotite (whole XML or PyRosetta script). Design and optimization operations are flagged as Rosetta-only rather than silently mistranslated.
Validation — validate_xml (optionally validate_against_schema, checking element names against the Rosetta XSD), rosetta_scripts_schema.
Environment — python_env_info, check_pyrosetta, install_pyrosetta_installer, find_rosetta_scripts.

Primary use cases: writing and debugging RosettaScripts protocols, scoring and relaxing structures with PyRosetta, porting Rosetta analysis code to the OSS Biotite stack.

Notes

The upstream README documents registration for Cursor; the snippets above are the Claude Code and Claude Desktop equivalents of that same stdio entry. Two environment variables carry all the configuration — PYTHON_BIN (the interpreter holding PyRosetta and Biotite) and ROSETTA_BIN (the compiled rosetta_scripts executable) — and getting either wrong is the usual cause of tools reporting the software as unavailable; python_env_info and check_pyrosetta exist to diagnose exactly that.

Rosetta itself is not bundled and is not free software: it is distributed under licence from the University of Washington (no cost for academic and non-commercial use, paid for commercial). The rosetta_to_biotite translation tools exist partly to give a licence-free path for the analysis half of a workflow — Biotite is BSD-3-Clause.

Complements the catalogued design-model wrappers ProteinMPNN, LigandMPNN and SolubleMPNN (sequence design), and the analysis-side PyMOL and MDAnalysis skills. No LICENSE file is committed upstream — see the pricing row.

Sources

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