Resolution:
## Figure 2.
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 |