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

Comparison of Segger and Other Methods for Segmentation and Rigid-Body Docking of Molecular Components in cryo-EM Density Maps

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Free PMC article
Comparative Study

Comparison of Segger and Other Methods for Segmentation and Rigid-Body Docking of Molecular Components in cryo-EM Density Maps

Grigore Pintilie et al. Biopolymers. .
Free PMC article

Abstract

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.

Figures

Figure 1
Figure 1
The top images shows the map of GroEL @4Å resolution (transparent surface), with Segger-docked models (ribbons with different colors for each protein), at 3 thresholds: 0.1, 0.7 and 1.25. The plot shows Atom Inclusion and Density Occupancy scores computed at evenly distributed thresholds for GroEL @4Å resolution, with a Segger-docked model. The threshold at which atom inclusion and density occupancy are balanced in this case is about 0.7 (middle image). The recommended threshold for visualizing this density map, as suggested by the authors of the density map, is 0.8, which is very close to this value.
Figure 2
Figure 2
Top 9 scores obtained while docking PDB:1XCK chain A into the density map of GroEL at 4.2Å resolution (EMDB: 5001) using Segger. The plots show that for all scores (cross-correlation, density occupancy, and clash score), the fit wit the top score has a significantly higher score than the next 8 top scores, which represent an incorrect or random placement of the structure in the density map.
Figure 3
Figure 3
(a) Density map and segmentation results for GroEL at 4.2Å resolution (EMDB:5001). (b) Segmented regions (transparent surfaces) from Segger, VolRover, and hENM is compared to the Segger-docked model (PDB:1XCK chain A). Red coloration signifies disagreement. (c) All 14 docked models of the same chain (random-colored ribbons) docked inside the density map (transparent surface), and an incorrectly docked model (red ribbon) along with symmetric copies (green ribbon) inside the map.
Figure 4
Figure 4
(a) Density map and segmentation results for GroEL+GroES at 7.7Å resolution (EMDB:1180). (b) Comparison of segmented regions from Segger and VolRover and docked models. (c) All Segger-docked models inside the density map.
Figure 5
Figure 5
(a) Density maps and segmentation results for GroEL at 23.5Å resolution (EMDB 1046). (b) Comparison of segmented regions from Segger and Volrover and the docked models. (c) All Segger-docked models inside the density map.
Figure 6
Figure 6
(a) Density map and segmentation results for Mm-cpn at 4.3Å resolution (EMDB:5001). (b) Comparison of segmented regions from Segger and Volrover and the docked models. (c) All Segger-docked models inside the density map.
Figure 7
Figure 7
(a) Segmentation and results for Mm-cpn at 8Å resolution (EMDB:5140). (b) Comparison of segmented regions from Segger and VolRover and Segger-docked models. (c) All Segger-docked models inside the density map.
Figure 8
Figure 8
(a) Density map and segmentation results for the rotavirus density map @3.8Å resolution (EMDB:1461). (b) Comparison between segmented regions and Segger-docked models. (c) All 3 Segger-docked models in the density map.
Figure 9
Figure 9
(a) Segmentation esults for Epsilon 15 @ 4.5Å resolution (EMDB:5003). (b) Comparison of Segger and VolRover regions and one of the docked models, and a Segger region after interactive modification based on the docked model. (c) All 7 Segger-docked models inside the asymmetric unit.
Figure 10
Figure 10
(a) Density map and segmentation results for Epsilon 15 @ 7.3Å resolution (EMDB:1557). (b) Comparisons of Segger and VolRover regions to one of the docked models. (c) All 7 Segger-docked models inside the asymmetric unit.
Figure 11
Figure 11
(a) Density map and segmentation results for Epsilon 15 @ 9.5Å resolution (EMDB:1176). (b) Comparisons of Segger and VolRover regions to docked models. (c) All 7 Segger-docked models inside the asymmetric unit.
Figure 12
Figure 12
(a) Density map and segmentation results for Ribosome at 7.4Å resolution (EMDB:1217). (b) Comparisons between segmented regions and the Segger-docked models. The first three images from the left show segmented regions and the large subunit (PDB:3JYW & 3JYX). The second three image show regions and the small subunit (PDB:3JYV). The rightmost image shows Segger regions and the docked models for PDB:2GO5 chains 4 and 5.
Figure 13
Figure 13
(a) Density map and segmentation results for Ribosome at 8.9Å resolution (EMDB:1345). (b) Comparisons between regions and the Segger-docked models. The first two images from the left show segmented regions and the large subunit (PDB:3JYW & 3JYX). The second two image show regions and the small subunit (PDB:3JYV). The rightmost image shows a Segger region and the docked model PDB:2P8W.
Figure 14
Figure 14
(a) Density map and segmentation results for Ribosome at 6.4Å resolution (EMDB:5030). (b) Comparisons between regions produced with Segger and VolRover compared to Segger-docked models.

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