// MCP TOOL REFERENCE

PROTEIN DESIGN TOOLS

19 tools from the Protein Design MCP Server, categorised by risk level.

// ALL 19 PROTEIN DESIGN TOOLS

READ 10 tools

Read analyze_interface Analyze protein-protein interface properties including buried surface area, Read get_design_status Check status of running design jobs for long-running operations. Read predict_affinity_boltz Predict binding affinity for a protein complex using Boltz. Read predict_structure Predict the 3D structure of a single protein chain using ESMFold or AlphaFold2. Read predict_structure_boltz Predict the 3D structure of a protein using Boltz (fast alternative to Read rosetta_interface_score Compute interface energy metrics for a protein complex using Rosetta. Read rosetta_score Score a protein structure using Rosetta energy function (ref2015). Read score_stability Score protein stability using ESM2 pseudo-log-likelihood. Read suggest_hotspots Analyze a target protein and suggest potential binding hotspots. Read validate_design Validate a designed protein sequence by predicting its structure with ESMFold

EXECUTE 9 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_design Fixed-backbone sequence design using Rosetta PackRotamers + MinMover. Execute rosetta_relax Relax a protein structure using Rosetta FastRelax protocol. Execute generate_backbone Generate de novo protein backbones using RFdiffusion.

// FAQ

How many tools does the Protein Design MCP server have? +

The Protein Design MCP server exposes 19 tools across 2 categories: Read, Execute.

How do I enforce policies on Protein Design tools? +

Route the Protein Design server through the PolicyLayer gateway. Define allow, deny, or approval rules per tool in the dashboard; they are enforced on every call before it reaches the server.

What risk categories do Protein Design tools fall into? +

Protein Design tools are categorised as Read (10), Execute (9). Each category has a recommended default policy.

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 →

Free to start. No card required.

43,000+ MCP servers and 220,000+ tools scanned and risk-classified.