Figure 3

The SurfaceAlign algorithm identifies the optimal alignment of spatially conserved residues. 6,220,800 alignment combinations and permutations are required for the alignment of 25 conserved residues of the heme binding pockets of myoglobin from P. catodon (a) and structural genomics target hemoglobin alpha-1 from P. flavescens (c). 100 alignment solutions are shown in stick representations (b). An alignment series shows the superposition of the solutions calculated towards converging to the optimal alignment (d). The myobglobin query surface is shaded in grayscale to represent the cRMSD values (black represents a large cRMSD and white represent small cRMSD) and the hemoglobin surface is colored by the shapely color scheme[77].