Figure 3

The thresholded affinity graph for the SSEF method. (a) The thresholded affinity graph for the SSEF method, where vertices are superfamilies in our dataset of 133 well populated CATH superfamilies and there is an edge between a pair of superfamilies if and only if both affinity scores are above a certain threshold. The threshold is such that 75% of self affinity scores, the affinity score of a superfamily to itself, are above this value. The superfamilies are color-coded according to the architecture group to which they belong. (Affinity graphs for the SEGF and LFF methods are given in the supplementary material [see Additional file 2].) (b)–(c) Structures of representative domains for some superfamilies involved in interesting interconnection patterns in the affinity graph. The affinity graph was drawn using Cytoscape [27]. The protein structures were rendered using PyMOL [26].