Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps.
Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Althoughα-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 ofβ-strands. The variety of shapes ofβ-sheets adds the complexity ofβ-strands detection from density maps. We propose a new approach to model traces ofβ-strands forβ-barrel density regions that are extracted from cryo-EM density maps. In the test containing eightβ-barrels extracted from experimental cryo-EM density maps at 5.5 Å-8.25 Å resolution,StrandRollerdetected about 74.26% of the amino acids in theβ-strands with an overall 2.05 Å 2-way distance between the detectedβ-traces and the observed ones, if the best of the fifteen detection cases is considered.
Division of Computing and Software Systems, University of Washington Bothell, Bothell, WA 98011, USA.
Dong
D
Si
Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA.
Jing
0000-0002-7249-4746
J
He
D003198:Computer Simulation; D020285:Cryoelectron Microscopy / Q000379:methods*; D030562:Databases, Protein; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D011506:Proteins