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Enables protein sequence analysis and structure prediction by extracting ESM-2 embeddings and batch processing FASTA files via Docker. It provides tools for lar
Enables protein sequence analysis and structure prediction by extracting ESM-2 embeddings and batch processing FASTA files via Docker. It provides tools for large-scale embedding extraction, job monitoring, and model management within an MCP-compatible environment.
Protein structure prediction using ESMFold via Docker
An MCP (Model Context Protocol) server for ESMFold protein analysis with 5 core tools:
The fastest way to get started. A pre-built Docker image is automatically published to GitHub Container Registry on every release.
# Pull the latest image
docker pull ghcr.io/macromnex/esmfold_mcp:latest
# Register with Claude Code (runs as current user to avoid permission issues)
claude mcp add esmfold -- docker run -i --rm --user `id -u`:`id -g` --gpus all --ipc=host -v `pwd`:`pwd` ghcr.io/macromnex/esmfold_mcp:latest
Note: Run from your project directory. `pwd` expands to the current working directory.
Requirements:
nvidia-docker or Docker with NVIDIA runtime)That's it! The ESMfold MCP server is now available in Claude Code.
Build the image yourself and install it into Claude Code. Useful for customization or offline environments.
# Clone the repository
git clone https://github.com/MacromNex/esmfold_mcp.git
cd esmfold_mcp
# Build the Docker image
docker build -t esmfold_mcp:latest .
# Register with Claude Code (runs as current user to avoid permission issues)
claude mcp add esmfold -- docker run -i --rm --user `id -u`:`id -g` --gpus all --ipc=host -v `pwd`:`pwd` esmfold_mcp:latest
Note: Run from your project directory. `pwd` expands to the current working directory.
Requirements:
About the Docker Flags:
-i — Interactive mode for Claude Code--rm — Automatically remove container after exit--user `id -u`:`id -g` — Runs the container as your current user, so output files are owned by you (not root)--gpus all — Grants access to all available GPUs--ipc=host — Uses host IPC namespace for better performance-v — Mounts your project directory so the container can access your dataAfter adding the MCP server, you can verify it's working:
# List registered MCP servers
claude mcp list
# You should see 'esmfold' in the output
In Claude Code, you can now use all 5 ESMfold tools:
extract_protein_embeddingssubmit_protein_embeddingssubmit_batch_protein_embeddingsget_job_statusget_job_resultOnce registered, you can use the ESMfold tools directly in Claude Code. Here are some common workflows:
I have protein sequences in /path/to/proteins.fasta. Can you extract ESM-2 embeddings using extract_protein_embeddings with the esm2_t33_650M_UR50D model and save the embeddings to /path/to/embeddings/?
I have a large dataset of 500 protein sequences in /path/to/large_dataset.fasta. Can you submit a batch embedding extraction job using submit_protein_embeddings with the esm2_t36_3B_UR50D model, then monitor the job until completion and retrieve the results?
I have variant sequences in /path/to/variants.fasta for a mutational study. Can you extract embeddings for all variants using extract_protein_embeddings and save to /path/to/variant_embeddings/ so I can compare them?
Docker not found?
docker --version # Install Docker if missing
GPU not accessible?
docker run --gpus all ubuntu nvidia-smiClaude Code not found?
# Install Claude Code
npm install -g @anthropic-ai/claude-code
Based on Meta AI Research (ESMFold/ESM-2)
Добавь это в claude_desktop_config.json и перезапусти Claude Desktop.
{
"mcpServers": {
"esmfold-mcp-server": {
"command": "npx",
"args": []
}
}
}