Direct conformational sampling from peptide energy landscapes through hypernetwork-conditioned diffusion

Abstract

Deep learning approaches have spurred substantial advances in the single-state prediction of biomolecular structures. The function of biomolecules is, however, dependent on the range of conformations they can assume. This is especially true for peptides, a highly flexible class of molecules that are involved in numerous biological processes and are of high interest as therapeutics. Here we introduce PepFlow, a transferable generative model that enables direct all-atom sampling from the allowable conformational space of input peptides. We train the model in a diffusion framework and subsequently use an equivalent flow to perform conformational sampling. To overcome the prohibitive cost of generalized all-atom modelling, we modularize the generation process and integrate a hypernetwork to predict sequence-specific network parameters. PepFlow accurately predicts peptide structures and effectively recapitulates experimental peptide ensembles at a fraction of the running time of traditional approaches. PepFlow can also be used to sample conformations that satisfy constraints such as macrocyclization. Modelling the different structures a peptide can assume is integral to understanding their function. The authors introduce PepFlow, a sequence-conditioned deep learning model that is shown to accurately and efficiently generate peptide conformations.