J Mol Biol. 2009 Sep 11;392(1):181-90. Epub 2009 Jul 8.

Refinement of protein structures into low-resolution density maps using rosetta.

DiMaio F, Tyka MD, Baker ML, Chiu W, Baker D.

Source

Department of Biochemistry, University of Washington, Seattle, 98195, USA. dimaio@u.washington.edu

Abstract

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 A resolution.

PMID:: 19596339; [PubMed - indexed for MEDLINE]

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