D2O Surrogate Model

This repository provides a surrogate Ridge model for predicting HDX–MS deuterium uptake from AlphaFold structures. It includes a Colab notebook for Stage‑1 (per‑residue predictions) and optional Stage‑2 correction against experimental data.

Features

• Stage‑1: compute residue features, predict rates & weights, output JSON and uptake plots.
• Stage‑2: load experimental CSV, map to peptides, apply correction model, output metrics and JSON.

Usage

1. Clone the repository:

   git clone https://github.com/YourUsername/D2O.git
   cd D2O_surrogate_model

2. Upload the directory to Colab.
3. Open D2O.ipynb, install dependencies, and follow these steps:
   • Enter the PDB path, Stage‑1 JSON, output directory, system label, and simulation parameters.
   • (Optional) Enter experimental CSV, Stage‑2 JSON, state filter, and exposure times.
4. Run the notebook cells to generate JSON outputs and accuracy plots.

Contributing

Issues and pull requests are welcome. Please do let me know how the results are for you!

Expect much more to come as I am finishing up the paper :)