Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in cryo-EM density maps

Biopolymers. 2012 Sep;97(9):742-60. doi: 10.1002/bip.22074.


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.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Antigens, Viral / chemistry
  • Capsid Proteins / chemistry
  • Chaperonin 10 / chemistry
  • Chaperonin 60 / chemistry
  • Cryoelectron Microscopy / methods*
  • Models, Molecular*
  • Ribosomes / ultrastructure


  • Antigens, Viral
  • Capsid Proteins
  • Chaperonin 10
  • Chaperonin 60
  • VP6 protein, Rotavirus