Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks
Figure 4
Illustrative examples of superposition of SVRs before and after realignment using PB approach.
The global superposition of protein structures before re-alignment is shown as cartoons in blue and red. The regions which were re-aligned locally are encircled. The local superposition is shown in ribbon representation. PB equivalences, scores and SDM values for bSVRs and aSVRs are also shown. This Figure and other figures showing an overlay of protein structures have been generated using Pymol software [82]. A–F: Examples of improved PB scores and SDM values using PB approach. G and H: Improved PB scores but an increase in SDM. Refer text for further details.