Rosetta/PyRosetta protein modeling and Biotite translation for computational biology
Most knowledge and memory work still happens through a UI a human drives. Rosetta MCP server moves it into the conversation instead. Rosetta/PyRosetta protein modeling and Biotite translation for computational biology.
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.
The server publishes 4 tools. What each one is for:
Cleanup — The Cleanup tool exposed by this serverDocumentation — The Documentation tool exposed by this serverTranslation — The Translation tool exposed by this serverEnvironment — The Environment tool exposed by this serverConfiguration is passed through the environment: ROSETTA_BIN, PYTHON_BIN. Treat anything key-shaped as a real credential — scope it to the minimum the server needs, and rotate it if it ever lands in a shared config.
rosetta-mcp-server on npm is all you need. Most clients run it directly, so configuration is a few lines and a restart.
Plenty of knowledge and memory servers cover similar ground. The differences that matter in practice are scope of access and how much setup stands between you and a working tool call. Rosetta's toolset — Cleanup, Documentation, Translation and 1 more — is a fair guide to whether it matches your workflow. It is maintained by Arielbs; worth a glance at recent repository activity before you build anything load-bearing on it.
SyncDev reviews every entry in this directory against the project's own documentation before publishing, and revisits them as servers change.
| Tool | What it does |
|---|---|
| Cleanup | The Cleanup tool exposed by this server. |
| Documentation | The Documentation tool exposed by this server. |
| Translation | The Translation tool exposed by this server. |
| Environment | The Environment tool exposed by this server. |
{
"mcpServers": {
"rosetta": {
"command": "rosetta-mcp-server",
"args": [],
"env": {
"ROSETTA_BIN": "/path/to/rosetta_scripts.default.macosclangrelease",
"PYTHON_BIN": "/path/to/.venvs/rosetta-mcp/bin/python"
}
}
}
}Configuration as documented by the project. Restart the client after saving.
| Variable | Description | Required |
|---|---|---|
| ROSETTA_BIN | Configuration value read at startup. | Optional |
| PYTHON_BIN | Configuration value read at startup. | Optional |
A knowledge graph your assistant keeps between sessions — entities, relations and observations that persist.
Kill hallucinated APIs — version-accurate, up-to-date library documentation injected straight into context.
Your workspace, on speaking terms with AI — search, read and write Notion pages and databases.
A structured scratchpad for hard problems — stepwise reasoning with revisions, branches and visible logic.
Symbol-level code navigation, refactoring and memory for coding agents — the IDE brain your assistant has been missing.
Chat with your second brain — search, read and write vault notes through the Local REST API.