Protein Conformational Transitions from All-Atom Adaptively Biased Path Optimization.

ABSTRACT: Simulation methods are valuable for elucidating protein conformational transitions between functionally diverse states given that transition pathways are difficult to capture experimentally. Nonetheless, specific computational algorithms are required because of the high free energy barriers between these different protein conformational states. Adaptively biased path optimization (ABPO) is an unrestrained, transition-path optimization method that works in a reduced-variable space to construct an adaptive biasing potential to aid convergence. ABPO was previously applied using a coarse-grained Go̅-model to study conformational activation of Lyn, a Src family tyrosine kinase. How effectively ABPO can be applied at the higher resolution of an all-atom model to explore protein conformational tr

SUBMITTER: Wu H 

PROVIDER: S-EPMC6358165 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature