Table 1.

Score from ROC curves and cumulative distributions distinguish structural alignment methods

Score with methoda
MEASURE	SSAP	STRUCTAL	DALI	LSQMAN	CE	SSM	Best-of-All
ROC area (native score)	0.83	0.94	0.94	0.70	0.89	0.80	NAb
ROC area (SAS score)	0.91	0.93	0.94	0.87	0.94	0.93	0.93
ROC area (GSAS score)	0.91	0.94	0.94	0.84	0.94	–	0.93
ROC area (SI score)	0.80	0.79	0.84	0.72	0.81	0.79	0.76
ROC area (MI score)	0.80	0.78	0.84	0.72	0.79	0.82	0.78
%TP at 1% FP (native score)	9	42	50	0.4	29	3	NA
%TP at 1% FP (SAS score)	48	32	47	29	46	25	22
%TP at 1% FP (GSAS score)	48	30	47	20	46	–	15
%TP at 1% FP (SI score)	16	2	16	4	9	0.8	1
%TP at 1% FP (MI score)	16	3	16	7	10	4	3
% CAT–CAT at GSAS=5 Å	19	68	37	29	50	–	74.0
% CAT–CAT at SAS=5 Å	25	80	62	54	61	73	85.7
% CAT–CAT at SI=5 Å	16	56	36	36	37	45	60.4
% CAT–CAT at MI=0.8	26	62	44	28	50	53	65.5
% All pairs at GSAS=5 Å	0.6	5.6	1.5	2.6	2.4	–	8.5
% All pairs at SAS=5 Å	0.8	9.4	3.5	5.6	3.5	7.1	13.5
% All pairs at SI=5 Å	1.4	17.2	4.7	11.1	6.1	13.8	24.2
% All pairs at MI=0.8	2.6	21.7	7.0	6.9	12.2	13.6	25.2

^aA high value is always better. The best scores for each measure are shown in bold, as are the scores for Best-of-All when they are the best.

^bThere is no native score for the Best-of-All method.