Table II.

Correlation between structural similarity scores

		β-barrels
		RMSD	TM-score	GDT_HA	GDT_TS	AL0	AL4	CAD
α-helical proteins	RMSD		-0.48	-0.37	-0.43	-0.44	-0.56	-0.42
	TM-score	-0.60		0.88	0.94	0.96	0.86	0.90
	GDT_HA	-0.60	0.85		0.98	0.93	0.76	0.97
	GDT_TS	-0.57	0.91	0.98		0.98	0.86	0.97
	AL0	-0.60	0.92	0.90	0.96		0.90	0.93
	AL4	-0.67	0.91	0.68	0.79	0.83		0.79
	CAD	-0.56	0.79	0.90	0.90	0.85	0.71

Pearson’s correlation coefficients (PCC) between structural similarity scores were calculated for a set of homology models of β-barrels (upper right), or α-helical proteins (lower left). RMSD and TM-score values are optimized in several of the structure alignment methods, whereas GDT, AL and CAD scores are used for assessment. Entries in bold indicate scores that are highly correlated with each other (PCC >0.9). Note that the RMSD values are negatively correlated with all other scores, because the RMSD has a maximum value of zero, whereas all other scores are inverted and rescaled to have a maximal value of 1.