This directory contains tutorials, accompanying data, and example results for various applications of the HDXer package. Each tutorial can be run within a self-contained Jupyter notebook, provided you have successfully installed the HDXer package in your Python environment.

All input data required to complete the tutorials is provided within this repository. However, in Tutorial 2 you are also given the option to recreate the input data using the trajectories provided in this Zenodo repository. It's not compulsory to download these trajectories, but you may find it useful, for example to check your understanding of the process, or to explore other HDXer functionalities.

• BPTI - Input data and example results for notebooks 1-5, studying BPTI with HDX experiments and HDXer
• notebooks/01_data_prep.ipynb - Tutorial 1, preparing experimental HDX data for use with HDXer
• notebooks/02_calc_hdx.ipynb - Tutorial 2, calculating HDX-MS data computationally from molecular dynamics trajectories
• notebooks/03_reweighting.ipynb - Tutorial 3 part 1, performing ensemble reweighting with the HDXer package, to fit an ensemble of structures that best describes a target (experimental) HDX-MS dataset
• notebooks/04_decision_plot.ipynb - Tutorial 3 part 2, assessing overfitting in HDXer ensemble reweighting using a decision plot
• notebooks/05_heatmap.ipynb - Tutorial 3 part 3, visualizing the effects of reweighting upon the agreement between computed and experimental HDX-MS