. 2017 Jan 1;24(1):52–67. doi: 10.1089/cmb.2016.0145

Table 2.

Helix Accuracy Measurement for Simulated Map-Structure Pairs Using Axis Length, the Two-Way Distance, the Arc Length, and the Sensitivity and Specificity of Detected Amino Acids

Helix ID^a	TL^b	DL^c	LDD^d	2-Way^e	C^f	L^g(Å)	P^h	Fpⁱor Sp_2.5^j	S_2.5^k
1FLP_1_4-19	23.54	23.04	Y	0.76	0.88	0.04	0.00	1	86.67
1FLP_2_21-35	20.71	19.98	Y	0.75	0.91	1.84	0.09	0	85.71
1FLP_3_37-41	5.99	15.06	N	2.24	0.62	10.54	0.67	4	100.00
1FLP_5_59-76	26.84	29.43	Y	0.57	0.74	2.59	0.09	2	94.12
1FLP_6_82-97	23.18	23.34	Y	0.74	0.77	2.54	0.10	0	100.00
1FLP_7-8_103-120	28.54	24.47	Y	0.60	0.79	3.56	0.13	0	94.12
1FLP_9-10_124-141	27.19	24.13	Y	0.78	0.99	2.32	0.09	0	76.47
1FLP Summary: 142 total AAs, 109 helix AAs				0.92	0.81	3.35	0.17	78.79	87.84
1HG5_1_20-29	14.02	17.18	Y	1.04	0.60	8.05	0.41	2	88.89
1HG5_2_39-49	15.89	20.82	Y	0.79	0.39	6.41	0.30	2	100.00
1HG5_3_56-66	15.93	18.40	Y	0.44	0.34	3.97	0.21	2	100.00
1HG5_4_72-88	24.83	20.67	Y	0.51	0.62	7.14	0.27	1	75.00
1HG5_5_91-99	12.82	11.30	Y	0.81	0.91	4.93	0.34	1	87.50
1HG5_6_115-141	41.70	35.76	N	0.37	0.54	5.38	0.13	0	96.15
1HG5_7_161-179	28.78	42.56	N	1.78	0.56	16.58	0.38	4	94.44
1HG5_9_191-221	46.59	48.69	Y	0.40	0.50	3.15	0.06	1	96.67
1HG5_10_229-257	44.29	41.59	Y	0.45	0.68	2.06	0.05	0	96.43
1HG5 Summary: 289 total AAs, 170 helix AAs				0.73	0.57	6.41	0.24	86.02	90.85
1UNF_1_37-43	9.10	N/A	N	N/A	N/A	N/A	N/A	0	0.00
1UNF_2_47-58	17.39	26.80	N	1.86	0.64	13.76	0.48	1	100.00
1UNF_3-4_69-80	18.78	13.66	Y	0.77	0.90	4.45	0.25	0	63.64
1UNF_5_85-100	23.10	24.11	Y	1.63	1.30	12.35	0.42	3	53.33
1UNF_6_112-122	15.66	N/A	N	N/A	N/A	N/A	N/A	0	0.00
1UNF_7_125-138	20.12	16.73	Y	0.33	0.40	2.86	0.15	0	100.00
1UNF_12_209-219	15.46	21.33	N	1.38	1.22	5.88	0.28	3	80.00
1UNF_13_223-237	21.81	17.75	Y	0.48	0.57	3.34	0.16	0	100.00
1UNF Summary: 238 total AAs, 111 helix AAs				1.08	0.84	7.11	0.29	92.23	68.37
2OVJ_2_364-376	18.85	16.45	Y	0.50	0.52	4.08	0.21	0	91.67
2OVJ_3_390-401	17.23	16.16	Y	0.50	0.69	0.65	0.04	0	100.00
2OVJ_5_415-427	18.84	23.23	Y	0.86	0.47	7.98	0.32	3	100.00
2OVJ_6_439-447	12.73	30.72	N	3.32	0.61	20.08	0.64	5	100.00
2OVJ_7_451-463	18.60	22.61	Y	0.76	0.79	4.01	0.18	1	83.33
2OVJ_8_467-485	27.74	32.53	Y	0.80	0.90	4.79	0.15	3	94.44
2OVJ_9_493-504	17.62	16.10	Y	0.65	0.77	1.11	0.06	1	90.91
2OVJ_10_514-533	30.84	29.02	Y	0.59	0.72	1.23	0.04	1	94.74
2OVJ_11-12_536-543	12.11	6.66	N	0.45	0.56	4.82	0.42	0	85.71
2OVJ Summary: 201 total AAs, 126 helix AAs				0.94	0.67	5.41	0.23	84.00	88.24
3E46_1_3-18	22.98	23.71	Y	0.72	0.76	4.05	0.16	0	93.33
3E46_4_106-118	19.14	17.87	Y	0.32	0.37	1.35	0.07	1	100.00
3E46_5_128-136	12.26	5.80	N	1.15	1.53	5.92	0.51	0	62.50
3E46_6_138-153	22.25	22.92	Y	1.44	1.85	5.57	0.22	0	73.33
3E46_7_160-171	16.91	15.78	Y	0.52	0.58	0.47	0.03	0	100.00
3E46_8_176-185	13.77	14.15	Y	0.75	0.81	2.05	0.14	0	100.00
3E46_9_190-199	13.99	13.32	Y	0.30	0.35	0.67	0.05	0	100.00
3E46 Summary: 253 total AAs, 93 helix AAs				0.74	0.89	2.87	0.17	99.08	84.88
1LWB_1_5-11	9.35	17.37	N	1.15	0.41	8.02	0.46	3	100.00
1LWB_2_17-28	17.16	15.05	Y	0.53	0.64	1.50	0.09	0	100.00
1LWB_3_30-36	10.94	N/A	N	N/A	N/A	N/A	N/A	0	0.00
1LWB_4_58-74	24.83	20.39	Y	0.50	0.60	3.85	0.16	0	87.50
1LWB_5_77-96	30.07	27.63	Y	0.46	0.54	3.04	0.10	0	89.47
1LWB_6_101-119	28.31	25.06	Y	0.99	1.24	5.09	0.17	0	77.78
1LWB Summary: 122 total AAs, 82 helix AAs				0.73	0.69	4.30	0.20	92.50	80.49
1NG6_1_3-16	20.04	19.08	Y	0.52	0.60	0.92	0.05	1	100.00
1NG6_2_20-39	29.44	28.12	Y	0.36	0.41	2.42	0.08	0	94.74
1NG6_3_47-71	37.38	35.36	Y	0.32	0.51	1.28	0.03	1	100.00
1NG6_4-5_74-90	26.00	23.28	Y	0.25	0.43	2.18	0.09	0	100.00
1NG6_6_97-110	20.06	18.00	Y	0.46	0.54	1.45	0.07	1	84.62
1NG6_7-8_116-130	23.58	17.79	N	0.73	0.86	5.26	0.23	0	78.57
1NG6_9_136-146	15.70	14.52	Y	0.28	0.35	0.52	0.03	1	100.00
1NG6 Summary: 148 total AAs, 116 helix AAs				0.42	0.53	2.00	0.08	87.50	92.24
3IEE_1_33-56	35.41	33.71	Y	0.53	0.67	1.25	0.04	1	95.65
3IEE_2_59-72	20.76	20.06	Y	0.76	0.91	2.45	0.11	0	91.67
3IEE_4_103-135	49.52	52.60	Y	0.68	0.79	6.13	0.11	2	90.63
3IEE_5_139-178	62.15	61.24	Y	0.47	1.25	1.61	0.03	1	97.37
3IEE_6_185-205	32.79	39.95	N	1.16	1.64	7.16	0.18	2	88.24
3IEE_7_213-231	28.08	29.62	Y	0.66	0.68	7.26	0.22	1	83.33
3IEE_8_240-263	36.41	42.32	N	0.84	1.07	5.91	0.14	3	95.45
3IEE_9_271-284	20.36	13.63	N	1.16	1.77	6.07	0.31	0	58.33
3IEE Summary: 270 total AAs, 193 helix AAs				0.78	1.10	4.73	0.14	75.81	88.71
1HZ4_1_5-24	29.43	26.67	Y	0.42	0.62	2.14	0.07	0	100.00
1HZ4_2_28-40	18.58	N/A	N	N/A	N/A	N/A	N/A	0	0.00
1HZ4_3_47-64	26.49	22.25	Y	0.50	0.60	3.54	0.14	0	88.24
1HZ4_4_67-83	24.48	24.29	Y	0.33	0.43	0.51	0.02	0	100.00
1HZ4_5_87-103	24.74	33.38	N	0.94	0.75	8.64	0.26	2	93.75
1HZ4_6_107-123	24.85	24.62	Y	0.35	0.48	0.45	0.02	0	100.00
1HZ4_7_131-145	22.07	N/A	N	N/A	N/A	N/A	N/A	0	0.00
1HZ4_8_149-162	20.15	20.98	Y	0.44	0.38	5.07	0.22	1	100.00
1HZ4_9-10_168-185	28.19	28.99	N	1.01	0.79	7.05	0.24	1	76.47
1HZ4_11_188-202	21.45	20.44	Y	0.44	0.52	3.68	0.16	0	92.86
1HZ4_12_209-225	24.89	22.98	Y	0.59	0.72	1.19	0.05	0	93.75
1HZ4_13_229-238	14.16	N/A	N	N/A	N/A	N/A	N/A	0	0.00
1HZ4_14-15_248-263	24.62	N/A	N	N/A	N/A	N/A	N/A	0	0.00
1HZ4_16_267-283	24.66	19.16	N	0.24	0.29	4.94	0.21	0	87.50
1HZ4_17_287-304	25.97	24.27	Y	0.40	0.46	3.51	0.13	1	94.12
1HZ4_18_307-324	26.86	21.02	N	0.27	0.38	5.23	0.20	0	88.24
1HZ4_20_334-346	18.59	18.67	Y	0.79	0.88	1.70	0.09	1	91.67
1HZ4_21_352-365	20.32	N/A	N	N/A	N/A	N/A	N/A	0	0.00
1HZ4 Summary: 366 total AAs, 291 helix AAs				0.52	0.56	3.67	0.14	92.00	68.99

Results computed with SSETracer.

^{^a}

PDB ID, the helix ID, and the first and last amino acid index for the helix. Sequentially adjacent helices that share the same direction are combined.

^{^b}

True length of the helix axis in the atomic model.

^{^c}

Detected length of the axis. N/A: Helix was not detected.

^{^d}

Length-difference detection. A helix is assumed to be detected when c-d ≤ 5.4 Å.

^{^e}

Averaged two-way distance (Eq. 4).

^{^f}

Lateral discrepancy C (Eq. 1).

^{^g}

Longitudinal discrepancy L (Eq. 2).

^{^h}

Proportion P of longitudinal discrepancy (Eq. 3).

^ⁱ

Number of false-positive nonhelix AAs (Eq. 6) within a specified radius (sheet AA: radius = 3.0 Å, loop AA: radius = 2.0 Å) of the detected helix axis.

^{^j}

Amino acid detection specificity (Eq. 6).

^{^k}

Amino acid detection sensitivity (Eq. 5).