Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps

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 compl...

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Bibliographic Details
Published in:BioMed research international 2017-01, Vol.2017 (2017), p.1-9
Main Authors: Si, Dong, He, Jing
Format: Article
Language:English
Subjects:
Amino acids
Biomedical research
Computer Simulation
Cryoelectron microscopy
Cryoelectron Microscopy - methods
Databases, Protein
Mathematical models
Methods
Physiological aspects
Protein Structure, Secondary
Proteins
Proteins - chemistry
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Summary: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.
ISSN:2314-6133
2314-6141
DOI:10.1155/2017/1793213