Distance distribution of aligned residue pairs. The structure pairs were superposed according to a given test or reference alignment and the distances between the C
atoms of aligned residue pairs were calculated. The residue pairs were then grouped into into distance bins of 0.5 Å size. Their relative frequency in each bin was plotted in logarithmic scale. The residue pairs 10 Å or more apart were collected in the last bin. The symbols and colors for methods are the same as in the Figure 7. The results from the reference alignment are shown by grey circles and lines. The inset shows the average alignment length of each method relative to that of the CDD alignment, where the method names on the x-axis were abbreviated by first two letters.