Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density MapsReport as inadecuate

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BioMed Research International - Volume 2017 2017, Article ID 1793213, 9 pages -

Research Article

Division of Computing and Software Systems, University of Washington Bothell, Bothell, WA 98011, USA

Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA

Correspondence should be addressed to Jing He

Received 15 September 2016; Accepted 8 December 2016; Published 10 January 2017

Academic Editor: Slavica Jonic

Copyright © 2017 Dong Si and Jing He. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Cryo-electron microscopy cryo-EM has produced density maps of various resolutions. Although α-helices can be detected from density maps at 5–8 Å resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5.5 Å–8.25 Å resolution, StrandRoller detected about 74.26% of the amino acids in the β-strands with an overall 2.05 Å 2-way distance between the detected β-traces and the observed ones, if the best of the fifteen detection cases is considered.

Author: Dong Si and Jing He



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