Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in cryo-EM density maps.
Segmentation and docking are useful methods for the discovery of molecular components in electron cryo-microscopy (cryo-EM) density maps of macromolecular complexes. In this article, we describe the segmentation and docking methods implemented in Segger. For 11 targets posted in the 2010 cryo-EM challenge, we segmented the regions corresponding to individual molecular components using Segger. We then used the segmented regions to guide rigid-body docking of individual components. Docking results were evaluated by comparing the docked components with published structures, and by calculation of several scores, such as atom inclusion, density occupancy, and geometry clash. The accuracy of the component segmentation using Segger and other methods was assessed by comparing segmented regions with docked components.
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA. pintilie@bcm.edu
Grigore
G
Pintilie
Wah
W
Chiu
D000956:Antigens, Viral / Q000737:chemistry; D036022:Capsid Proteins / Q000737:chemistry; D018835:Chaperonin 10 / Q000737:chemistry; D018834:Chaperonin 60 / Q000737:chemistry; D020285:Cryoelectron Microscopy / Q000379:methods*; D008958:Models, Molecular; D012270:Ribosomes / Q000648:ultrastructure
D000956:Antigens, Viral; D036022:Capsid Proteins; D018835:Chaperonin 10; D018834:Chaperonin 60; C061332:VP6 protein, Rotavirus