title: Tracing beta strands using StrandTwister from cryo-EM density maps at medium resolutions.
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 Å. 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 Å resolution and 39 β sheets computationally detected from cryo-EM density maps at 4.4-7.4 Å resolutions. Although experimentally derived cryo-EM maps contain errors, StrandTwister's best detections over 39 cases were able to detect 81.87% of the β strands, with an overall 1.66 Å 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.
authors.affiliation: Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA.
authors.forename: Dong
authors.initials: D
authors.lastname: Si
authors.affiliation: Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA. Electronic address: jhe@cs.odu.edu.
authors.forename: Jing
authors.initials: J
authors.lastname: He
mesh_terms: D000818:Animals; D020285:Cryoelectron Microscopy / Q000379:methods; D006801:Humans; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins