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 function
• translate_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.)

Improved: XML to PyRosetta translator

• 37 element types supported (was 6): 11 movers, 9 filters, 10 selectors, 7 task operations
• Full attribute handling: repeats, disable_design, cartesian, tolerance, threshold, distance, and more
• Child element support: MoveMap (with Span), Reweight, ScoreFunction
• Reports unrecognized elements so you know what needs manual work

Improved: Help and documentation

• get_rosetta_help now accepts any topic: movers by name ("FastRelax"), concepts ("constraints", "docking"), or score functions ("ref2015") -- auto-fetches live docs from rosettacommons.org
• search_rosetta_web_docs fallback: when DuckDuckGo is rate-limited, probes direct Rosetta docs URLs
• get_cached_docs auto-caches: no need to call cache_cli_docs first
• Expanded static help for score_functions, movers, filters, xml, and parameters

Improved: Scoring

• pyrosetta_score: new per_residue option returns per-residue energy breakdown
• scorefxn parameter now works (was ignored in v1.1.8)
• Proper error messages for missing files instead of silent {}

Improved: Validation

• validate_xml: new validate_against_schema option checks element names against the Rosetta XSD schema (catches typos like FastRleax)

MCP spec compliance fixes

• tools/call responses now use correct { content: [{ type: "text", text }] } format
• Tool errors return isError: true (not JSON-RPC errors)
• Standard JSON-RPC error codes (-32601, -32700, -32603)
• Removed false resources capability advertisement

Security fixes

• User input no longer interpolated into Python code (uses env vars / stdin)
• Temp files written to os.tmpdir() (not module directory)

Cleanup

• Removed 3 redundant tools: list_functions (merged into get_rosetta_info), search_pyrosetta_wheels, cache_cli_docs (auto-cache in get_cached_docs)
• Removed hardcoded personal paths
• Fixed shadowed variables, async anti-patterns, dead code
• 18 tools (was 21), all with improved agent-oriented descriptions

Example: asking a naive question

This is what makes the MCP server powerful -- an AI agent can answer domain questions by calling the right tools automatically:

User asks in Cursor: "How do I relax my protein and what's the Biotite equivalent?"

The agent calls two MCP tools behind the scenes:

1. get_rosetta_help("FastRelax") returns 6000+ chars of live documentation:

FastRelax performs all-atom relaxation using the FastRelax protocol. Parameters include scorefxn, repeats, cartesian, disable_design, MoveMap configuration...

2. rosetta_to_biotite("FastRelax") returns:

{
  "found": true,
  "results": [{
    "rosetta": { "name": "FastRelax", "example": ["relax = FastRelax()", "relax.set_scorefxn(get_score_function('ref

... [View full README on GitHub](https://github.com/Arielbs/rosetta-mcp-server#readme)