Evaluating the accuracy of protein design using native secondary sub-structures

Movahedi, Marziyeh; Zare-Mirakabad, Fatemeh; Arab, Seyed Shahriar

doi:10.1186/s12859-016-1199-y

BMC Bioinformatics

Table 3 Statistical assessment of designed sequences.

From: Evaluating the accuracy of protein design using native secondary sub-structures

PDB ID_Chain	E ^pot (a)				χ ² statistic (b)
PDB ID_Chain	Designed	Reference	Protein-like	Bunched	Designed	Reference	Uniprot-distributed
1ZZK_A	21.90	33.03	24.24	295.21	11.06	37.00	27.08
1XTE_A	41.57	42.78	32.98	429.21	23.28	26.14	15.31
1T3Y_A	46.15	40.46	43.67	652.03	22.07	21.70	8.88
1VQS_A	40.54	44.20	29.42	356.21	39.51	29.21	18.77
1OH0_A	45.88	29.85	34.79	438.79	37.73	25.73	12.06
1A2P_A	30.72	27.89	29.88	309.62	29.50	20.66	9.93
1EW4_A	28.98	35.20	37.23	347.37	17.05	36.39	10.05
1HZT_A	38.60	41.60	37.11	604.35	22.24	19.61	12.79
1IDP_A	46.38	37.74	43.54	634.46	50.10	36.94	17.01
1IUJ_A	38.96	31.30	34.49	402.85	32.30	30.23	21.15
1MG4_A	28.03	38.06	36.36	300.93	38.60	13.89	9.59
1NZ0_A	35.95	51.58	48.39	850.27	30.91	55.66	8.16
1URR_A	30.18	28.02	23.55	192.76	21.58	18.81	18.08
1VH5_A	43.58	33.43	37.03	595.33	27.32	15.73	30.65
1VKK_A	40.07	42.42	38.21	612.99	24.51	22.78	13.62
1WLU_A	38.57	40.23	36.69	613.45	40.15	25.25	13.47
1X6Z_A	32.58	44.50	35.98	642.98	27.93	28.63	29.13
1ZHV_A	38.18	67.38	47.61	722.31	22.84	23.84	17.15
2BWF_A	23.42	16.12	21.48	155.17	27.59	18.33	11.07
2FTR_A	49.27	21.01	36.12	290.87	77.06	34.49	15.43
2GPI_A	21.97	26.50	30.76	327.01	17.54	39.97	16.05
2PV2_A	30.48	32.50	32.56	318.45	24.16	13.83	13.01
3EBT_A	63.24	41.44	52.13	643.93	31.17	29.77	22.43
3EF8_A	56.73	46.87	43.06	704.12	36.44	23.44	19.55
3FEA_A	18.96	26.99	25.63	221.59	21.73	28.18	15.01
1GBS_A	72.44	56.16	46.31	1135.2	44.03	31.58	10.53
1R26_A	34.94	23.04	29.40	248.86	17.64	13.40	16.07
1Y25_A	48.29	53.31	52.55	1134.5	26.18	26.00	19.10
2PTH_A	66.33	77.51	58.86	1671.6	33.55	23.49	20.73
1ABA_A	22.67	18.05	19.76	166.69	15.93	16.75	11.94
1DBW_A	35.58	41.21	36.24	526.48	16.34	22.71	16.45
1I2T_A	34.03	34.00	23.55	182.00	20.22	20.07	10.84
1JF8_A	50.42	41.48	31.59	538.69	28.52	22.40	19.64
1KNG_A	47.69	47.33	39.62	777.74	20.34	24.70	13.16
2CAR_A	78.57	71.70	70.30	1603.3	31.39	26.90	13.87
1MF7_A	64.18	63.88	71.41	1550.0	29.86	20.98	16.92
1SHU_X	66.39	52.18	55.33	1426.0	16.93	19.34	15.08
1BKR_A	25.63	30.22	25.95	308.33	14.10	29.46	19.09
2GMY_A	37.04	34.64	35.70	604.25	29.84	16.53	8.61
1OAI_A	21.36	14.58	14.37	76.785	15.64	23.19	12.30
1UTG_A	23.59	22.73	20.83	142.38	33.41	18.75	16.26
1TQG_A	39.34	35.46	44.32	372.97	25.16	22.52	29.04
1TUK_A	15.96	21.39	25.78	190.00	8.20	73.94	26.47
1ZKE_A	52.57	26.50	39.81	282.41	56.29	24.02	16.89
2J5Y_A	19.41	18.76	23.69	156.59	23.08	19.26	22.90
2P5K_A	15.82	20.15	15.64	87.718	12.72	13.78	31.03
1GUT_A	20.80	34.68	33.24	276.11	24.02	18.78	11.73
2O1Q_A	42.20	35.61	42.15	634.86	33.39	35.21	14.52
3I4O_A	16.56	17.85	21.53	151.22	20.91	18.08	22.34
1EAQ_A	35.55	36.74	38.15	525.38	53.59	18.46	17.31
1JB3_A	35.90	38.39	33.32	444.65	25.70	21.64	14.12
1KMT_A	40.62	50.03	36.15	598.09	33.67	15.22	24.35
1KQ1_A	14.84	13.58	18.51	71.494	21.90	15.49	22.93
1NXM_A	61.59	60.02	60.89	1582.6	42.49	29.20	22.84
1O7I_A	35.83	38.47	43.29	571.87	20.76	21.11	19.77
1OK0_A	21.76	20.51	23.92	151.96	36.62	29.67	22.49
1QHQ_A	41.56	66.12	48.61	1052.2	19.43	59.80	15.67
1R6J_A	13.76	22.35	21.93	234.14	7.06	23.50	27.16
1UCS_A	12.26	20.15	19.60	150.73	21.99	29.24	16.83
2C9Q_A	34.82	31.49	33.78	416.12	22.62	33.69	16.02
2F01_A	33.91	32.49	41.94	632.93	44.30	69.50	17.83
2J2J_A	56.97	53.80	54.79	1232.2	29.27	44.44	14.14
2VMH_A	52.37	48.25	65.53	1022.4	48.85	31.09	23.27
3VUB_A	44.39	27.49	24.28	283.47	31.45	19.60	18.99
1M9Z_A	24.13	32.38	39.90	431.24	34.22	100.74	19.58
2J8B_A	22.71	21.00	24.56	264.71	28.96	105.67	14.13
2VOU_A	36.64	45.43	54.36	937.67	35.35	28.20	22.98
1V5I_B	28.93	20.44	28.45	145.74	31.51	11.70	15.60
2WLV_A	40.35	36.52	41.68	586.89	52.72	31.57	10.40
1F46_A	58.98	43.65	38.99	541.85	36.50	14.21	17.10
1VZI_A	33.33	37.45	42.36	578.66	63.84	39.32	18.86
2ANX_A	49.41	53.04	52.31	744.32	20.30	10.30	14.17
2CMP_A	25.96	25.58	31.02	154.14	19.60	18.92	10.19
2CVI_A	27.21	47.82	37.24	298.96	39.62	39.01	23.82
2D3D_A	27.45	28.78	35.66	306.37	18.22	22.52	15.46
2ERB_A	36.41	36.63	36.23	504.87	17.94	52.38	16.72
2O9S_A	16.01	13.43	15.44	100.61	59.57	14.03	9.57
2PR7_A	40.92	48.59	39.60	857.73	28.04	30.25	24.34
2QCP_X	19.48	19.43	22.94	150.64	25.94	18.24	15.44
2V1Q_A	14.77	19.23	19.72	98.525	20.10	18.11	16.45
2VPB_A	23.28	17.56	22.49	121.38	16.62	65.12	9.10
2VZC_A	40.47	40.82	51.30	660.83	16.20	33.51	20.36
2ZXY_A	31.88	25.72	31.14	312.36	24.89	22.00	21.61
3CTG_A	32.67	31.39	40.23	407.36	27.96	11.53	16.02
3E9T_A	29.23	38.88	39.61	488.97	21.08	28.89	21.48
3FIL_A	18.22	24.39	24.34	126.78	21.55	14.81	17.17
3G21_A	25.86	19.68	18.65	156.69	30.02	17.41	17.60
3G36_A	13.81	14.90	11.31	108.60	21.10	11.57	7.88
3IV4_A	35.41	25.83	31.88	388.37	31.85	26.41	9.82
Mean	35.64	35.30	35.58	498.34	28.71	28.16	17.08
Standard deviation	14.56	14.00	12.58	374.65	12.36	16.88	5.43
Quartile 1	23.59	24.39	24.56	221.59	20.76	18.75	13.47
Median	35.41	34.64	35.98	407.36	26.18	23.49	16.45
Quartile 3	42.20	42.78	42.15	634.46	33.55	30.25	20.36

(a) Pot statistic test penalizes short-range bunching of amino acids. The E ^pot value of reference and protein-like sequences give the minimal bunching. On the other hand, the maximal bunching is obtained from bunched sequences. The E ^pot values of designed sequences confirm that their bunching is typical of the native sequences. (b) Chi-square test is applied to determine if there is any significant difference between two sets of categorical data. The χ ² values indicate that the distribution of designed sequences versus Uniprot database is as significant as reference sequences

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