Refinement of protein structures into low-resolution density maps using rosetta.
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.
DiMaio
Frank
F
Department of Biochemistry, University of Washington, Seattle, 98195, USA. dimaio@u.washington.edu
Tyka
Michael D
MD
Baker
Matthew L
ML
Chiu
Wah
W
Baker
David
D
D020285:Cryoelectron Microscopy / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*
D011506:Proteins