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

J Mol Biol. 2009 Sep 11;392(1):181-90. doi: 10.1016/j.jmb.2009.07.008. Epub 2009 Jul 8.


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.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Cryoelectron Microscopy / methods*
  • Image Processing, Computer-Assisted / methods*
  • Proteins / chemistry*
  • Proteins / ultrastructure*


  • Proteins