A Pattern Recognition Tool for Medium-resolution Cryo-EM Density Maps and Low-resolution Cryo-ET Density maps.

Abstract

Cryo-electron microscopy (Cryo-EM) and cryo-electron tomography (cryo-ET) produce 3-D density maps of biological molecules at a range of resolution levels. Pattern recognition tools are important in distinguishing biological components from volumetric maps with the available resolutions. One of the most distinct characters in density maps at medium (5-10 Å) resolution is the visibility of protein secondary structures. Although computational methods have been developed, the accurate detection of helices and β-strands from cryo-EM density maps is still an active research area. We have developed a tool for protein secondary structure detection and evaluation of medium resolution 3-D cryo-EM density maps which combines three computational methods (SSETracer, StrandTwister, and AxisComparison). The program was integrated in UCSF Chimera, a popular visualization software in the cryo-EM community. In related work, we have developed BundleTrac, a computational method to trace filaments in a bundle from lower resolution cryo-ET density maps. It has been applied to actin filament tracing in stereocilia with good accuracy and can be potentially added as a tool in Chimera.