rosetta_design

THE RISK

High Risk

Why rosetta_design needs a policy

This tool executes computationally intensive external programs (Rosetta suite's PackRotamers and MinMover algorithms) to perform sequence design. It is not a simple data retrieval or write operation; it triggers an external computational workflow whose outputs depend on input arguments.

From the tool's definition 'Fixed-backbone sequence design using Rosetta PackRotamers + MinMover' — runs Rosetta computational design algorithms (PackRotamers + MinMover) which are external simulation/execution processes

Documented attack patterns abuse exactly the kind of access rosetta_design gives an agent:

POLICY

How to control rosetta_design

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_design:

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "rosetta_design": {
      "limits": [
        {
          "counter": "rosetta_design_rate",
          "window": "minute",
          "max": 10,
          "scope": "grant"
        }
      ]
    }
  }
}

rosetta_design stays usable, but rate-capped — a runaway agent can't fire it dozens of times a minute. Everything else on the server is denied unless you say otherwise.

Create a free account and register Protein Design — nothing to install.
Add this policy — paste it, or build it visually.
Point your MCP client (Claude, Cursor, anything) at your gateway URL.

RATE-LIMIT THIS TOOL →

Free to start. No card required.

EXPLORE

Related tools and policies

More Protein Design tools

Execute design_binder Design protein binders for a target protein. Runs complete pipeline: Execute design_fold End-to-end de novo fold design pipeline: RFdiffusion (unconditional backbone) → Execute design_sequence Design amino acid sequences for a protein backbone using ProteinMPNN. Execute energy_minimize Energy-minimize a protein structure using OpenMM with AMBER14 force field Execute optimize_sequence Optimize an existing binder sequence for improved stability and/or binding affinity. Execute predict_complex Predict the structure of a protein complex using AlphaFold2-Multimer. Execute rosetta_relax Relax a protein structure using Rosetta FastRelax protocol. Execute generate_backbone Generate de novo protein backbones using RFdiffusion.

All 19 Protein Design tools →

Execute tools on other servers

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Go deeper

High-risk tools in Protein Design → Every high-risk tool this server exposes, in one view.
All high-risk MCP tools → Every high-risk tool across the catalogue, and the policy pattern that contains them.
The MCP Attack Database → Documented attack patterns against MCP deployments — and the policies that stop them.
Agent sandbox → Bounding what an agent can execute and where the boundary should sit.
Least privilege for MCP → Granting agents the minimum tool surface the task needs.
Rate Limiting MCP Tool Calls: A Practical Guide →
MCP Security: Why Prompt Guardrails Aren't Enough →

FAQ

Questions about rosetta_design

What does the rosetta_design tool do? +

Fixed-backbone sequence design using Rosetta PackRotamers + MinMover. It is categorised as a Execute tool in the Protein Design MCP Server, which means it can trigger actions or run processes. Use rate limits and argument validation.

How do I enforce a policy on rosetta_design? +

Register the Protein Design MCP server in PolicyLayer and add a rule for rosetta_design: 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.

What risk level is rosetta_design? +

rosetta_design is a Execute tool with high risk. Execute tools should be rate-limited and have argument validation enabled.

Can I rate-limit rosetta_design? +

Yes. Add a rate_limit block to the rosetta_design 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.

How do I block rosetta_design completely? +

Set action: deny in the PolicyLayer policy for rosetta_design. 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.

What MCP server provides rosetta_design? +

rosetta_design 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.

Enforce policy on every Protein Design tool call.

Start from Protein Design, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.

CHECK YOUR STACK →