The plots of distributions of average structure overlap (within cut-off distances of 1Å, 2Å, and 3Å) of 435 pairwise alignments (all-against-all) of 30 randomly chosen structures from protein (A), DNA, RNA, and DNA-protein databases (B). The black lines show the average structure overlap at Z-score = 2.5 for the protein, DNA, RNA, DNA-protein databases. For the protein database (Figure 1A), the distribution of pairwise alignments of randomly chosen structures is in blue, and the distribution of 60 difficult pairwise alignments of homologous proteins (30% < SO < 70% and RMSD > 2.5Å) from HOMSTRAD database (http://tardis.nibio.go.jp/homstrad/) is in red. For the other databases (Figure 1B), the distribution of pairwise alignments of DNA, RNA, and DNA-protein is in purple, cyan, and green, respectively.