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

ABSTRACT: Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although ?-helices can be detected from density maps at 5-8?Å resolutions, ?-strands are challenging to detect at such density maps due to close-spacing of ?-strands. The variety of shapes of ?-sheets adds the complexity of ?-strands detection from density maps. We propose a new approach to model traces of ?-strands for ?-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight ?-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 ?-strands with an overall 2.05?Å 2-way distance between the detected ?-traces and the observed ones, if the best of the fifteen detection cases is considered.

SUBMITTER: Si D

PROVIDER: S-EPMC5259677 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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

Si Dong D He Jing J

BioMed research international 20170110

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 ...[more]

PMID: 28164115

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