Table 1.

Comparison of alignment accuracy on the 367 test proteins

Method	First threading alignment			Modeller model
	COV	GDT-HA	GDT-TS	COV	GDT-HA	GDT-TS
sp (FFAS)	0.81	35.02	47.34	0.85	34.33	47.31
sp + ss	0.84	36.42	49.07	0.88	35.67	49.07
sp + ss + sa	0.84	37.19	49.97	0.90	36.68	50.30
sp + ss + sa + rd	0.85	37.52	50.47	0.90	37.00	50.77
Re-ranking	0.89	39.08	52.42	0.94	38.19	52.40
HHpred	0.83	37.54	50.47	0.89	37.05	50.84

Note: COV, coverage; sp, sequence profile; ss, secondary structure; sa, solvent accessibility; rd, residue depth.