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

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Abstract

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.

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Si, D., & He, J. (2017). Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps. BioMed Research International, 2017. https://doi.org/10.1155/2017/1793213

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