Score a protein structure using Rosetta energy function (ref2015).
AI agents call rosetta_score to retrieve information from Protein Design without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
This tool evaluates/scores an existing protein structure using an energy function. It reads/analyzes a structure and returns a score — no data is modified, created, or deleted. Pure read/analysis operation with low blast radius.
From the tool's definition Score a protein structure using Rosetta energy function (ref2015)
Documented attack patterns abuse exactly the kind of access rosetta_score gives an agent:
PolicyLayer is an MCP gateway — it sits between your AI agents and Protein Design, and nothing reaches the server without passing your rules. This is the rule we recommend for rosetta_score:
{
"version": "1",
"default": "deny",
"tools": {
"rosetta_score": {}
}
}rosetta_score is read-only, so it stays allowed — but everything else on the server is denied unless you say otherwise.
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Score a protein structure using Rosetta energy function (ref2015). It is categorised as a Read tool in the Protein Design MCP Server, which means it retrieves data without modifying state.
Register the Protein Design MCP server in PolicyLayer and add a rule for rosetta_score: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches Protein Design. Nothing to install.
rosetta_score is a Read tool with low risk. Read-only tools are generally safe to allow by default.
Yes. Add a rate_limit block to the rosetta_score rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.
Set action: deny in the PolicyLayer policy for rosetta_score. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.
rosetta_score is provided by the Protein Design MCP server (jasonkim8652/protein-design-mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Start from Protein Design, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.
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19 Protein Design tools catalogued and risk-classified — across an index of 43,000+ MCP servers.