Rosetta ddG Calculation Pipeline 🧪

This repository provides a fully automated pipeline for evaluating the effects of point mutations on protein stability using Rosetta's ddG protocol. It is particularly useful in protein engineering, mutational screening, and stability prediction tasks.

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📁 Project Structure

├── Rosetta_ddG_calculations_for.ipynb
    └─ Jupyter Notebook for interactive analysis and visualization using PyRosetta
├── runddg_pal.py
│   └─ Main pipeline script: sets up structure, configures Rosetta runs, handles parallelization
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├── ana.py
│   └─ Parses Rosetta output to extract WT and mutant energies and compute ΔΔG

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⚙️ How to Use

1. Environment Setup

Requirements:

• Python 3.7+
• A compiled version of Rosetta (license required)
• PyRosetta (for visualization/analysis)
• Optional Python packages:

pip install matplotlib pandas jupyter

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⚠️ Notes

• Rosetta simulations are CPU-intensive; consider running on a cluster or high-performance workstation
• Make sure you have a legal license for Rosetta and PyRosetta
• .params files for ligands (if any) must be generated prior to running

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🧪 Suggested Workflow

1. Prepare initial structure and mutation list (Rosetta_ddG_calculations_for.ipynb)
2. Edit runddg_pal.py to match your setup
3. Run the runddg_pal.py script
4. Use ana.py to analyze and extract ΔΔG

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🧑‍💻 Authors & Contributions

• Script development: @VesperChen01 @yxl4567
• Feel free to contribute new analysis tools, visualization methods, or performance improvements!

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📄 License

This project is licensed under the MIT License.

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