Document Type
Article
Publication Date
2014
DOI
10.1016/j.str.2014.08.017
Publication Title
Structure
Volume
22
Issue
11
Pages
1665-1676
Abstract
Major secondary structure elements such as α helices and β sheets can be computationally detected from cryoelectron microscopy (cryo-EM) density maps with medium resolutions of 5–10 A˚ . However, a critical piece of information for modeling atomic structures is missing, because there are no tools to detect β strands from cryo-EM maps at medium resolutions. We propose a method, StrandTwister, to detect the traces of β strands through the analysis of twist, an intrinsic nature of a β sheet. StrandTwister has been tested using 100 β sheets simulated at 10 A˚ resolution and 39 β sheets computationally detected from cryo-EM density maps at 4.4–7.4 A˚ resolutions. Although experimentally derived cryoEMmaps contain errors, StrandTwister’s best detections over 39 cases were able to detect 81.87% of the β strands, with an overall 1.66 A˚ two-way distance between the detected and observed β traces. StrandTwister appears to detect the traces of β strands on major β sheets quite accurately, particularly at the central area of a β sheet.
Original Publication Citation
Si, D., & He, J. (2014). Tracing beta strands using StrandTwister from Cryo-EM density maps at medium resolutions. Structure, 22(11), 1665-1676. doi:10.1016/j.str.2014.08.017
Repository Citation
Si, D., & He, J. (2014). Tracing beta strands using StrandTwister from Cryo-EM density maps at medium resolutions. Structure, 22(11), 1665-1676. doi:10.1016/j.str.2014.08.017
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Comments
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