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Figure 4 | BMC Structural Biology

Figure 4

From: Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites

Figure 4

Calculating volume overlap between aligned surfaces. A surface on F420-0:gamma-glutamyl ligase homolog from A. fuldgidus (PDB:2g9i) (a) has a well conserved sub-surface (b, forest green) to the GDP binding surface in GDP-binding protein from B. taurus (c). A superposition of the surfaces from the alignment (d). When the volume overlap of the alignment is measured (e, purple), the large volume disparity between the surfaces masks the similarity with global surface volume overlap (gSVOT) score of 0.37. Using only the conserved residues of the alignment (f) to measure the local global volume overlap (lSVOT) reveals the similarity with lSVOT score of 0.71 (g, purple).

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