Foreword

These demo notebooks must be executed from the docs directory.

Before starting, remember to activate the environment:

source .venv/bin/activate

or equivalently

uv run jupyter notebook

The scripts also produce publication-quality figures in ../extra.

The original trajectories files are supporting information of the paper 1 and must be obtained from DESRES. They need to be split in 3 unfolded + 3 folded segments, downsampled, and filtered according to the directions in the files. For reproducibility, we provide the corresponding pre-computed projections (the high-dimensional embeddings that are input to the ID functions).

1. Lindorff-Larsen K, Piana S, Dror RO, Shaw DE. How Fast-Folding Proteins Fold. Science. 2011 Oct 28;334(6055):517–20.