Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy.

ABSTRACT: Advances in cryoelectron microscopy (cryo-EM) have revolutionized the structural investigation of large macromolecular assemblies. In this review, we first provide a broad overview of modeling methods used for flexible fitting of molecular models into cryo-EM density maps. We give special attention to approaches rooted in molecular simulations-atomistic molecular dynamics and Monte Carlo. Concise descriptions of the methods are given along with discussion of their advantages, limitations, and most popular alternatives. We also describe recent extensions of the widely used molecular dynamics flexible fitting (MDFF) method and discuss how different model-building techniques could be incorporated into new hybrid modeling schemes and simulation workflows. Finally, we provide two illustrative e

SUBMITTER: Dodd T 

PROVIDER: S-EPMC7284120 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature