title: Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.
abstract: Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data.
authors: University of Washington, Seattle, WA, United States; Institute for Protein Design, University of Washington, Seattle, WA, United States. Electronic address: dimaio@u.washington.edu.
authors: F
authors: F
authors: DiMaio
authors: National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX, United States. Electronic address: wah@bcm.edu.
authors: W
authors: W
authors: Chiu
mesh_terms: D000465:Algorithms; D000956:Antigens, Viral / Q000648:ultrastructure; D001426:Bacterial Proteins / Q000648:ultrastructure; D017795:Bromovirus / Q000648:ultrastructure; D036022:Capsid Proteins / Q000648:ultrastructure; D020285:Cryoelectron Microscopy / Q000295:instrumentation / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods / Q000706:statistics & numerical data*; D021621:Imaging, Three-Dimensional / Q000295:instrumentation / Q000379:methods; D008958:Models, Molecular; D011487:Protein Conformation; D012984:Software; D001616:beta-Galactosidase / Q000648:ultrastructure
chemical_list: D000956:Antigens, Viral; D001426:Bacterial Proteins; D036022:Capsid Proteins; C061332:VP6 protein, Rotavirus; D001616:beta-Galactosidase
keywords: CryoEM map-derived model; Model optimization; Model validation