Classical multidimensional scaling (MDS) plot of various automatically generated partitions and the SCOP fold partition. The MDS plot approximately preserves distances, Δ, between partitions (see Methods). The X axis represents the projection of the location of each partition onto the first eigenvector (first principal component), while the Y axis is a projection onto the second eigenvector (second principal component). The X and Y axes of the plot are scaled to represent the distance, Δ, divided by 1000. Automatic partitions are obtained with Ward's method clustering, based on two different similarity score for each of the three methods VAST, SHEBA and DALI. Each partition is designated by an uppercase letter: A, VAST Pcli Level cut; B, VAST Nres Level cut; C, DALI Zscore Level cut; D, DALI Nres Level cut; E, SHEBA Zscore Level cut; F, SHEBA Nres Level cut; G, VAST Pcli Largest Size cut; H, VAST Nres Largest Size cut; I, DALI Zscore Largest Size cut; J, DALI Nres Largest Size cut; K, SHEBA Zscore Largest Size cut; L, SHEBA Nres Largest Size cut, and S, the expert-curated partition SCOP. Automatic partitions resulting from the same tree-cutting strategy, are grouped together within the same dotted area.
Sam et al. BMC Bioinformatics 2008 9:74 doi:10.1186/1471-2105-9-74