protein-design-mcp 1.0.0

MCP server for protein design: RFdiffusion, ProteinMPNN, ESMFold, AlphaFold2, Boltz, PyRosetta, ESM2, OpenMM

Protein Design MCP Server

An MCP server that gives LLM agents access to computational protein design tools. Ask your LLM to design binders, generate de novo folds, predict structures, score interfaces, or relax with Rosetta — it calls the right tool automatically.

19 tools total, spanning generative design, structure prediction, physics-based scoring, and analysis. Built on RFdiffusion, ProteinMPNN, ESMFold, AlphaFold2, Boltz-2, PyRosetta, ESM2, and OpenMM.

Distribution	Tools out-of-the-box	Extras
pip install "protein-design-mcp[gpu]"	13 core tools	[rosetta] (license required), [boltz] (isolated venv)
docker pull jeonghyeonkim8652/protein-design-mcp	13 core tools (GPU), 10 (CPU)	PyRosetta / Boltz not bundled (license + torch conflict)

The 6 non-bundled tools (rosetta_* x4, predict_*_boltz x2) install cleanly via pip extras — see Optional Tools.

Installation

Choose the method that fits your situation. Listed from simplest to most customizable.

---

1. Auto-Setup (Recommended)

One command. Detects your environment, pulls Docker if available, writes MCP client config.

pip install protein-design-mcp
protein-design-mcp-setup

What it does:

• Checks for Docker and NVIDIA GPU
• Pulls the Docker image (or falls back to local Python mode)
• Writes config for Claude Desktop or Claude Code automatically
• Model weights download lazily on first tool call

Options:

protein-design-mcp-setup --docker    # Force Docker mode
protein-design-mcp-setup --local     # Force local Python mode
protein-design-mcp-setup --modal URL # Use Modal cloud GPU
protein-design-mcp-setup -y          # Skip confirmation prompt

---

2. Smithery

If you use Smithery:

npx -y @smithery/cli install protein-design-mcp --client claude

---

3. pip + Manual Config

pip install protein-design-mcp                      # Core CPU (10 tools)
pip install "protein-design-mcp[gpu]"               # + PyTorch + ESM (13 tools)
pip install "protein-design-mcp[gpu,rosetta]"       # + PyRosetta (17 tools) *
pip install "protein-design-mcp[gpu,rosetta,boltz]" # + Boltz-2 (all 19 tools) **

* PyRosetta requires a free academic license. The [rosetta] extra installs pyrosetta-installer which fetches the wheel after you accept the license.

** Boltz needs torch>=2.2 which conflicts with RFdiffusion's torch==2.0.1. Install in an isolated venv, not alongside [gpu].

Add to your MCP client config:

Claude Desktop (~/Library/Application Support/Claude/claude_desktop_config.json on macOS):

{
  "mcpServers": {
    "protein-design": {
      "command": "protein-design-mcp"
    }
  }
}

Claude Code (.mcp.json in your project root):

{
  "mcpServers": {
    "protein-design": {
      "command": "protein-design-mcp"
    }
  }
}

Restart your client after editing config.

---

4. Docker

Isolated, reproducible environments with all computational backends pre-installed. Primary registry: Docker Hub.

Pull

# Latest release (GPU image, ~12GB, bundles RFdiffusion + ProteinMPNN + ESMFold + ColabFold + ESM2 + OpenMM)
docker pull jeonghyeonkim8652/protein-design-mcp:latest
docker pull jeonghyeonkim8652/protein-design-mcp:1.0.0   # pin a specific version

GHCR mirror (equivalent):

docker pull ghcr.io/jasonkim8652/protein-design-mcp:latest

Tools included in the image: 13 of 19. The 6 license/conflict-gated tools (rosetta_*, predict_*_boltz) are not bundled — install via pip extras instead. See Optional Tools.

Run (GPU)

Model weights download lazily on first use and persist in a named volume so subsequent runs are instant:

docker volume create protein-design-models

docker run --rm -i \
  --gpus all \
  -v protein-design-models:/models \
  -v $(pwd):/data \
  jeonghyeonkim8652/protein-design-mcp:latest

GPU mode requires NVIDIA Container Toolkit. The image stdin/stdout is the MCP protocol — you normally don't run it directly, your MCP client does (see below).

Run (CPU)

No GPU — works with the same image:

docker run --rm -i \
  -e DEVICE=cpu \
  -v protein-design-models:/models \
  -v $(pwd):/data \
  jeonghyeonkim8652/protein-design-mcp:latest

CPU mode disables design_binder, design_fold, generate_backbone (RFdiffusion is GPU-only) → 10 tools available.

MCP client config

Claude Desktop (~/Library/Application Support/Claude/claude_desktop_config.json on macOS, or %APPDATA%/Claude/claude_desktop_config.json on Windows):

{
  "mcpServers": {
    "protein-design": {
      "command": "docker",
      "args": [
        "run", "-i", "--rm", "--gpus", "all",
        "-e", "SKIP_MODEL_DOWNLOAD=true",
        "-v", "protein-design-models:/models",
        "-v", "/absolute/path/to/your/pdbs:/data",
        "jeonghyeonkim8652/protein-design-mcp:latest"
      ]
    }
  }
}

Claude Code (.mcp.json in your project root):

{
  "mcpServers": {
    "protein-design": {
      "command": "docker",
      "args": [
        "run", "-i", "--rm", "--gpus", "all",
        "-v", "protein-design-models:/models",
        "-v", "${workspaceFolder}:/data",
        "jeonghyeonkim8652/protein-design-mcp:latest"
      ]
    }
  }
}

For CPU-only hosts, drop "--gpus", "all" and add "-e", "DEVICE=cpu".

Restart your MCP client after editing config.

Tags available on Docker Hub

Tag	Purpose
latest	Tracks the most recent release on main
1.0.0, 1.0, 1	Semver-pinned (recommended for production)
<sha>	Exact commit SHA (immutable)

Check the full tag list at hub.docker.com/r/jeonghyeonkim8652/protein-design-mcp/tags.

Build locally

git clone https://github.com/jasonkim8652/protein-design-mcp.git
cd protein-design-mcp
docker build -t protein-design-mcp:dev .                  # GPU image
docker build -f Dockerfile.lite -t protein-design-mcp:lite .  # CPU-only, ~3-5GB

The GPU build needs ~30 GB free disk and ~20 minutes.

---

5. Modal (Cloud GPU)

No local GPU? Deploy to your own Modal account. Serverless GPU on demand, billed per-second (~$1.10/hr A10G). Containers auto-stop after 5 min idle.

pip install modal
modal setup                          # One-time: link your Modal account

git clone https://github.com/jasonkim8652/protein-design-mcp.git
cd protein-design-mcp
pip install -e .
modal deploy deploy/modal_app.py     # Deploy GPU endpoint

After deploying, Modal prints your endpoint URL. Connect via the local proxy:

{
  "mcpServers": {
    "protein-design": {
      "command": "python",
      "args": ["-m", "protein_design_mcp.modal_proxy"],
      "env": {
        "MODAL_URL": "https://<your-workspace>--protein-design-tools.modal.run"
      }
    }
  }
}

All 19 tools available. Local PDB files are automatically sent to Modal.

---

6. From Source (Development)

git clone https://github.com/jasonkim8652/protein-design-mcp.git
cd protein-design-mcp
pip install -e ".[gpu,dev]"
python -m protein_design_mcp.server

For full GPU pipeline, install RFdiffusion and ProteinMPNN separately and set RFDIFFUSION_PATH / PROTEINMPNN_PATH.

---

CPU vs GPU

	GPU	CPU
Tools available	All 19	14 (no design_binder, design_fold, generate_backbone, predict_structure_boltz, predict_affinity_boltz)
RFdiffusion	~30s/design	Disabled
Boltz-2	~10-30s	Disabled
ESMFold	~10s	~2-5min
ESM2	~5s	~30s
ProteinMPNN	~30s	~5-10min
PyRosetta	Fast	Comparable
OpenMM	Fast	Comparable
AlphaFold2 (API)	Works	Works

GPU is auto-detected. To force CPU mode, set DEVICE=cpu.

Available Tools

Tools marked (optional) are not bundled in the Docker image. See Optional Tools for install.

Design & Generation

design_binder (GPU only)

End-to-end binder design: RFdiffusion (backbone) -> ProteinMPNN (sequence) -> ESMFold (validation).

{
  "target_pdb": "path/to/target.pdb",
  "hotspot_residues": ["A45", "A46", "A49"],
  "num_designs": 10,
  "binder_length": 80
}

Returns ranked designs with sequences, PDB structures, pLDDT, pTM, and mpnn_score.

generate_backbone (GPU only)

De novo backbone generation using unconditional RFdiffusion. No target protein required.

{"length": 100, "num_designs": 5}

design_fold (GPU only)

End-to-end de novo fold design: RFdiffusion (unconditional backbone) → ProteinMPNN (sequence) → AlphaFold2 (validation, falls back to ESMFold). Returns ranked designs filtered by pLDDT/pTM.

{"length": 120, "num_designs": 10, "num_sequences_per_backbone": 4}

design_sequence

Design sequences for a given backbone using ProteinMPNN. Unlike optimize_sequence (which refines an existing sequence), this designs from scratch given only a backbone PDB — the correct tool after generate_backbone. Optionally validates each design with ESMFold.

{
  "backbone_pdb": "path/to/backbone.pdb",
  "num_sequences": 8,
  "sampling_temp": 0.1,
  "fixed_positions": [1, 5, 10],
  "validate": true
}

optimize_sequence

Redesign a protein sequence for improved stability and/or binding affinity using ProteinMPNN.

{
  "current_sequence": "MTKLYV...",
  "target_pdb": "path/to/target.pdb",
  "optimization_target": "both",
  "fixed_positions": [1, 5, 10]
}

Structure Prediction

predict_structure

Single-chain structure prediction via ESMFold (fast) or AlphaFold2 (accurate).

{"sequence": "MTKLYV...", "predictor": "esmfold"}

Returns PDB file, mean pLDDT, pTM, per-residue confidence.

predict_complex

Multi-chain complex structure prediction using AlphaFold2-Multimer.

{
  "sequences": ["BINDER_SEQ...", "TARGET_SEQ..."],
  "chain_names": ["binder", "target"]
}

Returns predicted complex PDB with pLDDT, pTM/ipTM, and PAE matrix.

predict_structure_boltz (GPU only, optional)

Single-chain structure prediction with Boltz-2 — a fast, high-accuracy open model competitive with AF2.

{"sequence": "MTKLYV...", "model": "boltz2", "num_samples": 1}

Returns predicted PDB, mean pLDDT, pTM.

predict_affinity_boltz (GPU only, optional)

Multi-chain complex + binding affinity prediction with Boltz-2. Returns affinity score alongside the predicted complex structure and confidence metrics.

{"sequences": ["BINDER_SEQ...", "TARGET_SEQ..."], "model": "boltz2"}

validate_design

Predict structure of a designed sequence and optionally compute RMSD against a reference.

{
  "sequence": "MTKLYV...",
  "expected_structure": "path/to/reference.pdb",
  "predictor": "esmfold"
}

Analysis & Scoring

analyze_interface

Analyze protein-protein interface: contacts, buried surface area, hydrogen bonds, salt bridges.

{"complex_pdb": "path/to/complex.pdb", "chain_a": "A", "chain_b": "B"}

suggest_hotspots

Predict binding hotspots from multiple sources. Accepts protein names, UniProt IDs, PDB IDs, or file paths.

{"target": "EGFR", "criteria": "druggable", "include_literature": true}

Criteria: "exposed" (SASA), "druggable" (pocket geometry), "conserved" (evolution).

score_stability

Protein stability scoring via ESM2 pseudo-log-likelihood. Optionally score individual mutations.

{
  "sequence": "MTKLYV...",
  "mutations": ["A42G", "L55V"]
}

Returns overall stability score and per-mutation delta log-likelihood (stabilizing/destabilizing).

energy_minimize

All-atom energy minimization with OpenMM (AMBER14 + implicit solvent).

{"pdb_path": "path/to/structure.pdb", "num_steps": 500, "solvent": "implicit"}

Returns minimized PDB, energy change, and RMSD from input.

Rosetta (Physics-Based Design & Scoring) — optional

PyRosetta-backed tools for physics-based scoring, relaxation, and fixed-backbone design. All use ref2015 by default. Not bundled in Docker — install via pip install "protein-design-mcp[rosetta]" after accepting the PyRosetta license.

rosetta_score

Score a structure with a Rosetta energy function. Returns total score, per-residue energies, and component breakdown.

{"pdb_path": "path/to/structure.pdb", "score_function": "ref2015"}

rosetta_relax

FastRelax protocol to find a low-energy conformation. Returns relaxed PDB, energy before/after, and CA-RMSD from input.

{"pdb_path": "path/to/structure.pdb", "nstruct": 1}

rosetta_interface_score

Interface analysis via InterfaceAnalyzerMover: binding energy (dG_separated), buried surface area (dSASA), interface hydrogen bonds, packstat.

{"pdb_path": "path/to/complex.pdb", "chains": "A_B"}

rosetta_design

Fixed-backbone redesign pipeline: score → PackRotamers → MinMover → score. Returns designed PDB, mutation list, and energy delta. Composite tool — in benchmark mode, call rosetta_score / rosetta_relax individually instead.

{"pdb_path": "path/to/input.pdb", "chains": "A_B", "fixed_positions": [12, 14, 18]}

Utility

get_design_status

Check progress of long-running design jobs.

{"job_id": "abc123"}

Optional Tools: PyRosetta + Boltz-2

These 6 tools (rosetta_score, rosetta_relax, rosetta_interface_score, rosetta_design, predict_structure_boltz, predict_affinity_boltz) are not included in the Docker image because:

• PyRosetta requires a Rosetta license (free for academics, paid for commercial) and cannot be legally redistributed in a container.
• Boltz-2 needs torch>=2.2, while RFdiffusion's dependency chain (e3nn, dgl) pins torch==2.0.1. Both cannot coexist in one venv.

Installing PyRosetta tools

1. Register at pyrosetta.org/downloads and accept the license.
2. Install alongside the MCP server:

   pip install "protein-design-mcp[gpu,rosetta]"
   python -c "import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()"
   

3. Verify: python -c "import pyrosetta; print(pyrosetta.__version__)"

The 4 rosetta_* tools become available immediately.

Installing Boltz-2 tools

Create a separate virtualenv (isolated from the RFdiffusion torch stack):

python -m venv ~/.venvs/protein-design-boltz
source ~/.venvs/protein-design-boltz/bin/activate
pip install "protein-design-mcp[boltz]"

Then point your MCP client at this venv's protein-design-mcp binary (or run two MCP servers — one for RFdiffusion/Docker tools, one for Boltz).

Configuring two MCP servers side-by-side

{
  "mcpServers": {
    "protein-design": {
      "command": "docker",
      "args": ["run", "-i", "--rm", "--gpus", "all",
               "-v", "protein-design-models:/models",
               "jeonghyeonkim8652/protein-design-mcp:latest"]
    },
    "protein-design-boltz": {
      "command": "/home/you/.venvs/protein-design-boltz/bin/protein-design-mcp"
    }
  }
}

Your LLM will see all 19 tools through the two servers and call whichever is appropriate.

Configuration

Variable	Description	Default
DEVICE	"auto", "cuda", or "cpu"	auto
RFDIFFUSION_PATH	Path to RFdiffusion installation	/opt/RFdiffusion
PROTEINMPNN_PATH	Path to ProteinMPNN installation	/opt/ProteinMPNN
COLABFOLD_BACKEND	"api" (remote MSA) or "local" (local DB)	api
CACHE_DIR	Cache directory	~/.cache/protein-design-mcp
TORCH_HOME	ESM model weights directory	(PyTorch default)
SKIP_MODEL_DOWNLOAD	Skip eager weight download in Docker	true

Architecture

MCP Server (stdio)
 |
 +-- Design tools
 |    +-- design_binder         RFdiffusion -> ProteinMPNN -> ESMFold
 |    +-- design_fold           RFdiffusion -> ProteinMPNN -> AlphaFold2
 |    +-- generate_backbone     RFdiffusion (unconditional)
 |    +-- design_sequence       ProteinMPNN (+ optional ESMFold validation)
 |    +-- optimize_sequence     ProteinMPNN + ESMFold
 |
 +-- Structure prediction
 |    +-- predict_structure       ESMFold or AlphaFold2
 |    +-- predict_complex         AlphaFold2-Multimer (ColabFold)
 |    +-- predict_structure_boltz Boltz-2 (monomer)
 |    +-- predict_affinity_boltz  Boltz-2 (complex + affinity)
 |    +-- validate_design         Structure prediction + RMSD
 |
 +-- Rosetta (PyRosetta)
 |    +-- rosetta_score           ref2015 energy scoring
 |    +-- rosetta_relax           FastRelax
 |    +-- rosetta_interface_score InterfaceAnalyzerMover
 |    +-- rosetta_design          PackRotamers + MinMover
 |
 +-- Analysis tools
 |    +-- analyze_interface   PDB geometry analysis
 |    +-- suggest_hotspots    SASA + pockets + UniProt + PubMed
 |    +-- score_stability     ESM2 pseudo-log-likelihood
 |    +-- energy_minimize     OpenMM (AMBER14)
 |
 +-- Utilities
      +-- get_design_status  Job queue polling
      +-- Structure fetching (RCSB, AlphaFold DB, UniProt)
      +-- Conservation scoring, caching

Development

git clone https://github.com/jasonkim8652/protein-design-mcp.git
cd protein-design-mcp
pip install -e ".[gpu,dev]"

pytest tests/           # Run tests
ruff check .            # Lint
black .                 # Format
mypy src/               # Type check

License

Apache License 2.0 - see LICENSE for details.

References

• MCP Specification
• RFdiffusion - Protein backbone generation
• ProteinMPNN - Sequence design
• ESMFold / ESM2 - Structure prediction and stability scoring
• ColabFold - Fast AlphaFold2 with MMseqs2
• Boltz - Open structure and affinity prediction
• PyRosetta - Physics-based protein modeling
• OpenMM - Molecular dynamics and energy minimization