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Biophys J. 2017 Jun 20;112(12):2479-2493. doi: 10.1016/j.bpj.2017.04.054.

Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences.

Author information

1
Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri. Electronic address: hangdou@gmail.com.
2
Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri.
3
Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas.

Abstract

Although electron cryo-microscopy (cryo-EM) has recently achieved resolutions of better than 3 Å, at which point molecular modeling can be done directly from the density map, analysis and annotation of a cryo-EM density map still primarily rely on fitting atomic or homology models to the density map. In this article, we present, to our knowledge, a new method for flexible fitting of known or modeled protein structures into cryo-EM density maps. Unlike existing methods that are guided by local density gradients, our method is guided by correspondences between the α-helices in the density map and model, and does not require an initial rigid-body fitting step. Compared with current methods on both simulated and experimental density maps, our method not only achieves greater accuracy for proteins with large deformations but also runs as fast or faster than many of the other flexible fitting routines.

PMID:
28636906
PMCID:
PMC5479111
DOI:
10.1016/j.bpj.2017.04.054
[Indexed for MEDLINE]
Free PMC Article

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