Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta

JOURNAL OF MOLECULAR BIOLOGY

卷:392

Article

DiMaio, Frank¹  Tyka, Michael D.¹  Baker, Matthew L.²  Chiu, Wah²  Baker, David¹ 

[1] Univ Washington, Dept Biochem, Seattle, WA 98195 USA

[2] Baylor Coll Med, Natl Ctr Macromol Imaging, Verna & Marrs McLean Dept Biochem & Mol Biol, Houston, TX 77030 USA

关键词: cryoEM;    density fitting;    structure prediction;    Rosetta;    comparative modeling;   

DOI  :  10.1016/j.jmb.2009.07.008

来源: Elsevier

【 摘 要 】

We describe a method based on Rosetta structure refinement for generating high-resolution, all-atom protein models from electron cryomicroscopy density maps. A local measure of the fit of a model to the density is used to directly guide structure refinement and to identify regions incompatible with the density that are then targeted for extensive rebuilding. Over a range of test cases using both simulated and experimentally generated data, the method consistently increases the accuracy of starting models generated either by comparative modeling or by hand-tracing the density. The method can achieve near-atomic resolution starting from density maps at 4-6 angstrom resolution. (C) 2009 Elsevier Ltd. All rights reserved.

【 授权许可】

Free