Table 1.

Z-scores for all helical class topologies in test set A: scores obtained for each topology for Blosum62, VT160_RA, and VTML200 matrices are shown in columns 2, 3, and 4

	Z-score
Topology	Blosum62	VT160_RA	VTML200	Blosum62 combined		VT160_RA combined
				Max z-score	Max % improvement	Max z-score	Max % improvement
1.10.10	1.24	1.43	1.23	2.37	65.8	2.37	66.10
1.10.30	1.19	1.33	1.21	1.90	42.5	1.95	46.11
1.10.150	1.28	1.41	1.30	2.42	71.4	2.44	72.17
1.10.238	0.73	0.88	0.77	1.42	61.0	1.46	65.87
1.10.260	0.65	0.68	0.66	1.04	52.1	1.03	51.36
1.10.375	0.96	1.10	0.97	1.54	40.3	1.55	40.85
1.10.490	1.29	1.46	1.33	1.84	26.1	1.86	27.15
1.10.533	1.00	1.05	1.03	1.60	52.5	1.60	52.85
1.10.555	1.47	1.87	1.46	2.74	46.8	2.77	48.21
1.10.565	0.89	1.44	1.02	1.88	29.9	1.91	32.21
1.10.600	1.72	2.21	1.66	2.79	25.9	2.76	24.83
1.10.620	2.60	3.09	2.76	3.11	0.8	3.11	0.88
1.10.760	0.49	0.54	0.51	0.56	3.9	0.56	4.12
1.10.1170	0.37	0.41	0.38	1.82	339.8	1.75	322.87
1.10.1200	0.95	1.03	0.99	1.13	10.1	1.17	13.22
1.10.1220	0.94	1.04	0.98	1.07	3.4	1.11	6.46
1.10.1300	3.34	3.60	3.32	3.64	1.3	3.60	0.24
1.10.3210	0.75	0.80	0.72	1.35	69.4	1.37	71.22
1.20.20	1.68	1.85	1.66	2.81	51.5	2.83	52.81
1.20.920	1.68	1.88	1.69	3.28	74.5	3.29	74.93
1.20.1070	2.85	3.32	2.84	3.66	10.3	3.67	10.52
1.20.1250	0.79	0.78	0.79	1.13	43.4	1.11	40.92
1.25.40	0.76	1.11	0.61	2.54	129.3	2.50	125.62

Columns 5 and 6 show the maximum z-score obtained and the maximum percent improvement obtained when using Blosum62 combined with topology-based matrices. Columns 7 and 8 show the show the maximum z-scores obtained and the maximum percentage improvements obtained when using VT160_RA combined with topology-based matrices. Maximum percent improvement is the improvement of combined topology-based matrices over the maximum z-score giving generic matrix for each topology. Only the topologies where z-score improvements were observed for both Blosum62 combined and VT160_RA combined matrices over all three of the generic matrices are shown