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Enables protein stability prediction ($DeltaDelta$G and $Delta$Tm) and systematic mutation analysis using the SPIRED-Stab deep learning model. It supports singl
Enables protein stability prediction ($DeltaDelta$G and $Delta$Tm) and systematic mutation analysis using the SPIRED-Stab deep learning model. It supports single variant analysis, batch processing, and job monitoring via Docker-based inference.
Protein stability prediction using SPIRED-Stab deep learning model via Docker
An MCP (Model Context Protocol) server for protein stability prediction with 6 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/spired_stab_mcp:latest
# Register with Claude Code (runs as current user to avoid permission issues)
claude mcp add spired_stab -- docker run -i --rm --user `id -u`:`id -g` --gpus all --ipc=host -v `pwd`:`pwd` ghcr.io/macromnex/spired_stab_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 SPIRED-Stab 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/spired_stab_mcp.git
cd spired_stab_mcp
# Build the Docker image
docker build -t spired_stab_mcp:latest .
# Register with Claude Code (runs as current user to avoid permission issues)
claude mcp add spired_stab -- docker run -i --rm --user `id -u`:`id -g` --gpus all --ipc=host -v `pwd`:`pwd` spired_stab_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 PyTorch shared memory-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 'spired_stab' in the output
In Claude Code, you can now use all 6 SPIRED-Stab tools:
predict_stabilityanalyze_single_variantsubmit_stability_predictionsubmit_batch_mutation_analysisget_job_statusget_job_resultOnce registered, you can use the SPIRED-Stab tools directly in Claude Code. Here are some common workflows:
I have protein variants at /path/to/variants.csv with a 'seq' column and wild-type sequence at /path/to/wt.fasta. Can you use predict_stability to predict stability changes for all variants and save results to /path/to/results.csv?
I want to analyze the effect of mutation I31L on my protein. The wild-type sequence is at /path/to/wt.fasta. Can you use analyze_single_variant to predict the stability change for this mutation?
I want to explore all possible mutations at positions 31, 67, and 124 of my protein at /path/to/wt.fasta. Can you submit a batch mutation analysis job using submit_batch_mutation_analysis with max 100 variants, and monitor progress until completion?
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
Out of GPU memory?
device: "cpu" for CPU inference (significantly slower)submit_stability_prediction for background processingResearch use — Based on SPIRED-Stab by YoGo-1030.
Добавь это в claude_desktop_config.json и перезапусти Claude Desktop.
{
"mcpServers": {
"spired-stab-mcp": {
"command": "npx",
"args": []
}
}
}