Assessments of Variational Autoencoder in Protein Conformation Exploration

Molecular dynamics (MD) simulations have been extensively used to study protein dynamics and subsequently functions. However, MD simulations are often insufficient to explore adequate conformational space for protein functions within reachable timescales. Accordingly, many enhanced sampling methods, including variational autoencoder (VAE) based methods, have been developed to address this issue. The purpose of this study is to evaluate the feasibility of using VAE to assist in the exploration of protein conformational landscapes. Using three modeling systems, we showed that VAE could capture high-level hidden information which distinguishes protein conformations. These models could also be used to generate new physically plausible protein conformations for direct sampling in favorable conformational spaces. We also found that VAE worked better in interpolation than extrapolation and increasing latent space dimension could lead to a trade-off between performances and complexities.