Figure 1

The relative performance of the methods, comparing the ROC ₃₀₀ score across superfamilies. There is one scatter plot per pair of methods: SSEF and SEGF (a), SSEF and LFF (b), and SEGF and LFF (c). Each superfamily is a point on the plot with the coordinates being the ROC₃₀₀ scores of the corresponding methods. For a pair of methods, groups whose position significantly deviates from the main diagonal are examples of relative strength and weakness of the methods; for every pair of methods, six superfamilies that deviate the most from the diagonal are listed in the table adjacent to the plot. The superfamilies are colored according to the minimum SSAP score for a pair of domains in the superfamily as reported by the DHS database [23]: blue for scores in (0.0, 53.44], green for scores in (53.44, 63.32], orange for scores in (63.32, 73.48], and red for scores in (73.48, 100.00]. The SSAP (Sequential Structure Alignment Program) method [24] is a robust protein structure alignment method that uses a double dynamic programming strategy to align protein structures. The SSAP score measures the structural similarity on a scale from 100.0 (the most similar) to 0.0 (the least similar). Our chosen threshold values, 53.44, 63.32, and 73.48, correspond to the 25th, 50th, and 75th percentile respectively. The superfamilies for which the SSAP scores are not available are colored black. The correlation between the performance of every pair of methods is captured by Pearson correlation coefficient which is shown in upper left corner of the corresponding plots.