Construction of protein backbone pieces using segmentbased FBCCD and Cryo-EM skeleton

Cryo-Electron Microscopy is a biophysical technique that generates volumetric images of macromolecules. Although it is hard to distinguish the backbone from the density map at medium resolutions such as 5-10Å, the location of major secondary structure traces and the skeleton can be detected from such density maps. We introduce an effective method to construct pieces of backbone conformations for α-helices, β-strands and loops using α-traces, β-traces and skeleton trace that can be detected from a density map. A test of nineteen cases shows that our fragmentbased FBCCD method can quickly build a model that aligns well with a spline trace with a small RMSD from the native.