Comparison of the quality of the alignments produced by the methods SSAP, STRUCTAL, DALI, LSQMAN, CE, and SSM, using four geometric match measures: GSAS, SAS, SI, and MI. For each geometric measure and for each method, we plot a cumulative distribution. This gives the number of alignments (expressed as a percentage of the total number of alignments in the set considered) that is found with a geometric match score better than the particular threshold plotted along the *x*-axis. A lower value of the geometric match measure is better in all cases. In the upper panels, we consider the set of 104,309 pairs that have the same Class/Architecture/Topology (CAT) classification; in the lower panels we consider all pairs (these number 4,290,985). Better performing methods find more alignments (greater values along the *y*-axis) with better scores (smaller values on *x*-axis). The MI measure is always between 0 and 1, whereas the other measures are unbounded. For GSAS, SAS, and SI, we use a cutoff value 5 Å, which allows us to focus on good matches. The Figure also shows the cumulative distribution of the Best-of-All method, a method that returns the best alignment found by any of the above methods. This method is clearly the best performer in all categories. Among the existing methods, for each of the geometric match measures, STRUCTAL is the best performer; the next best method is SSM.

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