Rosetta Mcp Server
This server bridges AI assistants to the Rosetta computational biology suite and Biotite library. It exposes 18 tools that let you run RosettaScripts XML protocols, score structures with PyRosetta, validate XML against schema, and translate between Rosetta and Biotite APIs. The translation tools are notable: they map 37 XML element types to PyRosetta code and provide bidirectional lookups between Rosetta functions and their Biotite equivalents, complete with working examples. You also get live documentation fetching from rosettacommons.org, per-residue energy breakdowns, and automatic PyRosetta installation. Reach for this when you want an LLM to help write or debug protein modeling pipelines without hallucinating API signatures or guessing which operations Biotite actually supports.
- GitHub stars
- 16
- tools
- 18
- transport
- STDIO
- env vars
- 3
- last updated
- Apr 3, 2026
Tools
18 toolsPublic tool metadata for what this MCP can expose to an agent.
get_rosetta_infoAll available score functions, movers, filters, selectors, parameters
All available score functions, movers, filters, selectors, parameters
No parameter schema in public metadata yet.
get_rosetta_helpHelp for any topic -- accepts mover names, concepts, or score functions
Help for any topic -- accepts mover names, concepts, or score functions
No parameter schema in public metadata yet.
pyrosetta_introspectLive PyRosetta API search with docs and signatures
Live PyRosetta API search with docs and signatures
No parameter schema in public metadata yet.
search_rosetta_web_docsSearch rosettacommons.org documentation
Search rosettacommons.org documentation
No parameter schema in public metadata yet.
get_rosetta_web_docFetch and read a specific docs page
Fetch and read a specific docs page
No parameter schema in public metadata yet.
get_cached_docsSearch cached CLI help (auto-caches on first use)
Search cached CLI help (auto-caches on first use)
No parameter schema in public metadata yet.
run_rosetta_scriptsRun a RosettaScripts XML protocol on a PDB
Run a RosettaScripts XML protocol on a PDB
No parameter schema in public metadata yet.
pyrosetta_scoreScore a PDB with optional per-residue breakdown
Score a PDB with optional per-residue breakdown
No parameter schema in public metadata yet.
xml_to_pyrosettaXML to PyRosetta Python (37 element types)
XML to PyRosetta Python (37 element types)
No parameter schema in public metadata yet.
rosetta_to_biotiteFind Biotite equivalent of a Rosetta function
Find Biotite equivalent of a Rosetta function
No parameter schema in public metadata yet.
biotite_to_rosettaFind Rosetta equivalent of a Biotite function
Find Rosetta equivalent of a Biotite function
No parameter schema in public metadata yet.
translate_rosetta_script_to_biotiteTranslate full scripts from Rosetta to Biotite
Translate full scripts from Rosetta to Biotite
No parameter schema in public metadata yet.
validate_xmlCheck XML syntax + optional schema validation
Check XML syntax + optional schema validation
No parameter schema in public metadata yet.
rosetta_scripts_schemaGenerate XSD schema and extract element names
Generate XSD schema and extract element names
No parameter schema in public metadata yet.
python_env_infoPython version and installed packages
Python version and installed packages
No parameter schema in public metadata yet.
check_pyrosettaVerify PyRosetta is available
Verify PyRosetta is available
No parameter schema in public metadata yet.
install_pyrosetta_installerAuto-install PyRosetta (10-30 min)
Auto-install PyRosetta (10-30 min)
No parameter schema in public metadata yet.
find_rosetta_scriptsLocate the rosetta_scripts binary
Locate the rosetta_scripts binary
No parameter schema in public metadata yet.
Sponsors
Agent CaffeineSponsoredClose your lid, come back to finished work
SnugSponsoredThe clipboard manager for the AI eraPromote your product hereReach 125k+ visitors monthly
WaxSponsoredBlock anything with supervision, without erasing your iPhonePromote your product hereReach 125k+ visitors monthly
knobsSponsoredSee your site on any phone, any day, in any languageConfiguration
ROSETTA_BINPath to rosetta_scripts binary or its directory
PYTHON_BINPython interpreter with PyRosetta/Biotite installed
MCP_DEBUGSet to 1 for debug logging
Readme
Rosetta MCP Server
Rosetta MCP Server
Author: Ariel J. Ben-Sasson
A Model Context Protocol (MCP) server that lets Cursor (or any MCP client) work with Rosetta, PyRosetta, and Biotite: run RosettaScripts, validate XML protocols, translate between Rosetta and Biotite, score structures, and query documentation -- all from your AI coding assistant.
What's new in v1.3.0 (vs v1.1.8 on npm)
New: Biotite integration
rosetta_to_biotite-- Find the Biotite equivalent of any Rosetta function with working example code (21 mappings covering structure I/O, SASA, RMSD, superimposition, secondary structure, contacts, hydrogen bonds, B-factors, angles, and more)biotite_to_rosetta-- Reverse lookup: find the Rosetta equivalent of a Biotite functiontranslate_rosetta_script_to_biotite-- Translate entire RosettaScripts XML or PyRosetta code to Biotite Python. Design/optimization operations are flagged as Rosetta-only.- Fuzzy search with keyword aliases ("contacts", "binding energy", "surface area", "align", etc.)
Details
- Repository
- github.com/arielbs/rosetta-mcp-server
- Package
rosetta-mcp-server- Transport
- STDIO
- Registry
- MCP registry, active