A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps.

ABSTRACT: The rapid progress of cryo-electron microscopy (cryo-EM) in structural biology has raised an urgent need for robust methods to create and refine atomic-level structural models using low-resolution EM density maps. We propose a new protocol to create initial models using I-TASSER protein structure prediction, followed by EM density map-based rigid-body structure fitting, flexible fragment adjustment and atomic-level structure refinement simulations. The protocol was tested on a large set of 285 non-homologous proteins and generated structural models with correct folds for 260 proteins, where 28% had RMSDs below 2 Å. Compared to other state-of-the-art methods, the major advantage of the proposed pipeline lies in the uniform structure prediction and refinement protocol, as well as the extensi

SUBMITTER: Zhang B 

PROVIDER: S-EPMC7502543 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature