ProtScape: A molecular structure and energy-aware representation for protein conformation generation

Excerpt

arXiv:2410.20317v2 Announce Type: replace Abstract: Molecular dynamics (MD) simulations are a principled but computationally expensive approach for studying protein conformational variability, making it challenging to generate large ensembles of structures or characterize transitions between metastable conformations. AI methods for upsampling MD simulations have been developed recently but struggle due to difficulties of sampling complex, high-dimensional molecular distributions. One avenue thes