Structural comparison of the backbone in the presence of ligand-induced conformational changes. Illustrations of results from the default ProSMART comparison of open (PDB entry 2cex
chain A) and closed (PDB entry 3b50
chain A) forms of the SiaP TRAP sialic acid-binding protein, coloured using a colour gradient according to main-chain dissimilarity scores (yellow implies similarity and red relative dissimilarity; white, not applicable). Since the two models do not superpose well, for clarity only 2cex
chain A is shown in (b)–(d). The Procrustes score (b) allows easy identification of locally distorted regions (such as hinges). The Flexible score (c) helps to identify regions that are at all similar, despite any global conformational change (note that the whole structure is coloured yellow, indicating high local similarity despite different global conformations). The Hinging score (d) is useful for identifying subtle backbone deformations (including hinges) that can otherwise be very hard to identify. These complementary depictions allow quick visual identification of exactly which regions are structurally very similar and which exhibit differences. (a) Open (2cex
chain A, left) and closed (3b50
chain A, right) forms of SiaP. (b) Coloured by the Procrustes score. (c) Coloured by the Flexible score. (d) Coloured by the Hinging score.