Table 2 Benchmarking results for Apo-Holo datasets using the Hetero FNAT and iRMSD models.

From: Classification and prediction of protein–protein interaction interface using machine learning algorithm

Actual native	Actual non-native		Probability threshold	Accuracy	TP	TN	FP	FN	TPR (sensitivity)	TNR (specificity)	NPV	Precision	F1 score	MCC
Apo-Holo dataset defined by FNAT (native: original and one with FNAT ≥ 0.80 overlap and non-native: ten with FNAT ≤ 0.25 overlap with original complex interface)
FNAT_Model (native: original and one from FNAT ≥ 0.80 overlap and non-native: FNAT ≤ 0.25 overlap with original complex interface; ratio: 1:5)
56	280		0.50	93.738	44.340	270.620	9.380	11.660	0.792	0.966	0.959	0.826	0.808	0.771
56	280		0.55	93.640	43.290	271.340	8.660	12.710	0.773	0.969	0.955	0.834	0.802	0.765
56	280		0.60	93.479	42.070	272.020	7.980	13.930	0.751	0.971	0.951	0.841	0.793	0.757
56	280		0.65	93.271	40.690	272.700	7.300	15.310	0.727	0.974	0.947	0.848	0.782	0.746
56	280		0.70	93.024	39.150	273.410	6.590	16.850	0.699	0.976	0.942	0.857	0.769	0.734
56	280		0.75	92.735	37.340	274.250	5.750	18.660	0.667	0.979	0.936	0.867	0.753	0.720
56	280		0.80	92.271	35.040	274.990	5.010	20.960	0.626	0.982	0.929	0.876	0.729	0.699
56	280		0.85	91.688	32.400	275.670	4.330	23.600	0.579	0.985	0.921	0.883	0.698	0.673
56	280		0.90	90.914	29.080	276.390	3.610	26.920	0.519	0.987	0.911	0.890	0.655	0.637
56	280		0.95	89.756	24.350	277.230	2.770	31.650	0.435	0.990	0.898	0.899	0.585	0.581
Apo-Holo dataset defined by FNAT (native: original and one with FNAT ≥ 0.80 overlap and non-native: ten with FNAT ≥ 0.25 and ≤ 0.50 overlap with original complex interface)
FNAT_Model (native: original and one from FNAT ≥ 0.80 overlap and non-native: FNAT ≥ 0.25 and ≤ 0.5 overlap with original complex interface; ratio: 1:5)
10	50		0.50	91.467	4.970	49.910	0.090	5.030	0.497	0.998	0.909	0.985	0.659	0.664
10	50		0.55	91.417	4.910	49.940	0.060	5.090	0.491	0.999	0.908	0.990	0.655	0.662
10	50		0.60	91.300	4.810	49.970	0.030	5.190	0.481	0.999	0.906	0.995	0.647	0.657
10	50		0.65	91.233	4.750	49.990	0.010	5.250	0.475	1.000	0.905	0.998	0.642	0.655
10	50		0.70	90.967	4.590	49.990	0.010	5.410	0.459	1.000	0.902	0.998	0.627	0.643
10	50		0.75	90.750	4.450	50.000	0.000	5.550	0.445	1.000	0.900	1.000	0.613	0.633
10	50		0.80	90.383	4.230	50.000	0.000	5.770	0.423	1.000	0.897	1.000	0.592	0.616
10	50		0.85	89.867	3.920	50.000	0.000	6.080	0.392	1.000	0.892	1.000	0.559	0.591
10	50		0.90	88.883	3.330	50.000	0.000	6.670	0.333	1.000	0.883	1.000	0.493	0.542
10	50		0.95	87.133	2.280	50.000	0.000	7.720	0.228	1.000	0.866	1.000	0.365	0.444
Apo-Holo dataset defined by FNAT (native: original and one with FNAT ≥ 0.80 overlap and non-native: ten with FNAT ≥ 0.50 and ≤ 0.80 overlap with original complex interface)
FNAT_Model (native: original and one from FNAT ≥ 0.80 overlap and non-native: FNAT ≥ 0.50 and ≤ 0.80 overlap with original complex interface; ratio: 1:5)
20	100	0.50		78.083	15.33	78.37	21.63	4.67	0.767	0.784	0.944	0.416	0.538	0.444
20	100	0.55		78.592	14.51	79.8	20.2	5.49	0.726	0.798	0.936	0.419	0.530	0.430
20	100	0.60		79.108	13.69	81.24	18.76	6.31	0.685	0.812	0.928	0.423	0.521	0.417
20	100	0.65		79.650	13.07	82.51	17.49	6.93	0.654	0.825	0.923	0.428	0.516	0.409
20	100	0.70		80.108	12.17	83.96	16.04	7.83	0.609	0.840	0.915	0.432	0.503	0.394
20	100	0.75		80.467	10.99	85.57	14.43	9.01	0.550	0.856	0.905	0.431	0.482	0.370
20	100	0.80		80.842	9.94	87.07	12.93	10.06	0.497	0.871	0.897	0.432	0.460	0.349
20	100	0.85		80.692	8.35	88.48	11.52	11.65	0.418	0.885	0.884	0.416	0.415	0.303
20	100	0.90		80.967	6.84	90.32	9.68	13.16	0.342	0.903	0.873	0.409	0.370	0.265
20	100	0.95		81.400	4.87	92.81	7.19	15.13	0.244	0.928	0.860	0.407	0.299	0.213
Apo-Holo dataset defined by FNAT (native: original and one with FNAT ≥ 0.80 overlap and non-native: ten with FNAT < 0.80 overlap with original complex interface)
FNAT_Model (native: original and one from FNAT ≥ 0.80 overlap and non-native: FNAT < 0.80 overlap with original complex interface; ratio: 1:5)
64	320	0.50		89.547	46.48	297.38	22.62	17.52	0.726	0.929	0.944	0.674	0.698	0.636
64	320	0.55		89.672	44.82	299.52	20.48	19.18	0.700	0.936	0.940	0.687	0.693	0.631
64	320	0.60		89.797	43.23	301.59	18.41	20.77	0.675	0.942	0.936	0.703	0.688	0.627
64	320	0.65		89.755	41.3	303.36	16.64	22.7	0.645	0.948	0.930	0.714	0.677	0.618
64	320	0.70		89.784	39.47	305.3	14.7	24.53	0.617	0.954	0.926	0.730	0.667	0.611
64	320	0.75		89.695	37.18	307.25	12.75	26.82	0.581	0.960	0.920	0.746	0.652	0.600
64	320	0.80		89.563	34.52	309.4	10.6	29.48	0.539	0.967	0.913	0.767	0.632	0.586
64	320	0.85		89.357	31.8	311.33	8.67	32.2	0.497	0.973	0.906	0.789	0.608	0.570
64	320	0.90		89.013	28.29	313.52	6.48	35.71	0.442	0.980	0.898	0.817	0.572	0.548
64	320	0.95		88.292	23.05	315.99	4.01	40.95	0.360	0.987	0.885	0.855	0.505	0.506
Apo-Holo dataset defined by iRMSD (native: original and one with iRMSD ≤ 5 Å overlap and non-native: ten with iRMSD > 15 Å with original complex interface)
iRMSD_Model (native: original and one from iRMSD ≤ 5 Å overlap and non-native: iRMSD > 15 Å overlap with original complex interface; ratio: 1:5)
98	490		0.5	80.2	402.44	87.56	17.8	82.08	0.82	0.82	0.49	0.96	0.61	0.53
98	490		0.55	76.88	421.08	68.92	21.12	84.69	0.78	0.86	0.54	0.95	0.63	0.56
98	490		0.6	73.96	433.36	56.64	24.04	86.28	0.75	0.88	0.57	0.95	0.65	0.58
98	490		0.65	69.76	442.08	47.92	28.24	87.05	0.71	0.90	0.60	0.94	0.65	0.58
98	490		0.7	66.28	447.2	42.8	31.72	87.33	0.68	0.91	0.62	0.93	0.64	0.57
98	490		0.75	61.88	455.56	34.44	36.12	88.00	0.63	0.93	0.65	0.93	0.64	0.57
98	490		0.8	57	464.84	25.16	41	88.75	0.58	0.95	0.70	0.92	0.63	0.57
98	490		0.85	51.12	472.44	17.56	46.88	89.04	0.52	0.96	0.75	0.91	0.61	0.57
98	490		0.9	43.6	479.68	10.32	54.4	88.99	0.44	0.98	0.82	0.90	0.57	0.55
98	490		0.95	31.76	486.84	3.16	66.24	88.20	0.32	0.99	0.91	0.88	0.48	0.50
Apo-Holo dataset defined by iRMSD (native: original and one with iRMSD ≤ 5 Å overlap and non-native: ten with iRMSD > 10 Å and ≤ 15 Å overlap with original complex interface)
iRMSD_Model (native: original and one from iRMSD ≤ 5 Å overlap and non-native: iRMSD > 5 Å and ≤ 10 Å overlap with original complex interface; ratio: 1:5)
134	680		0.5	126.52	483.76	196.24	7.48	74.97	0.94	0.71	0.39	0.98	0.55	0.50
134	680		0.55	124.56	501.56	178.44	9.44	76.92	0.93	0.74	0.41	0.98	0.57	0.51
134	680		0.6	122.6	520.8	159.2	11.4	79.04	0.91	0.77	0.44	0.98	0.59	0.53
134	680		0.65	120.16	532.4	147.6	13.84	80.17	0.90	0.78	0.45	0.97	0.60	0.54
134	680		0.7	117.4	551	129	16.6	82.11	0.88	0.81	0.48	0.97	0.62	0.55
134	680		0.75	114.04	565.76	114.24	19.96	83.51	0.85	0.83	0.50	0.97	0.63	0.56
134	680		0.8	109.28	583.24	96.76	24.72	85.08	0.82	0.86	0.53	0.96	0.64	0.57
134	680		0.85	102.6	604.6	75.4	31.4	86.88	0.77	0.89	0.58	0.95	0.66	0.59
134	680		0.9	94.08	628.36	51.64	39.92	88.75	0.70	0.92	0.65	0.94	0.67	0.61
134	680		0.95	75.84	653	27	58.16	89.54	0.57	0.96	0.74	0.92	0.64	0.59
Apo-Holo dataset defined by iRMSD (native: original and one with iRMSD ≤ 5 Å overlap and non-native: ten with iRMSD > 5 Å and ≤ 10 Å overlap with original complex interface)
iRMSD_Model (native: original and one from iRMSD ≤ 5 Å overlap and non-native: iRMSD > 10 Å and ≤ 15 Å overlap with original complex interface; ratio: 1:5)
134	680	0.5		129.52	380.88	299.12	4.48	62.70	0.97	0.56	0.30	0.99	0.46	0.39
134	680	0.55		128.04	397.72	282.28	5.96	64.59	0.96	0.58	0.31	0.99	0.47	0.40
134	680	0.6		126.68	418.12	261.88	7.32	66.93	0.95	0.61	0.33	0.98	0.49	0.42
134	680	0.65		124.2	436.12	243.88	9.8	68.84	0.93	0.64	0.34	0.98	0.50	0.43
134	680	0.7		122.24	457.04	222.96	11.76	71.16	0.91	0.67	0.36	0.97	0.51	0.44
134	680	0.75		118.08	479.52	200.48	15.92	73.42	0.88	0.71	0.37	0.97	0.52	0.45
134	680	0.8		113	503.64	176.36	21	75.75	0.84	0.74	0.39	0.96	0.54	0.45
134	680	0.85		105.48	532.28	147.72	28.52	78.35	0.79	0.78	0.42	0.95	0.55	0.46
134	680	0.9		95.28	568.56	111.44	38.72	81.55	0.71	0.84	0.47	0.94	0.56	0.47
134	680	0.95		75.92	615.28	64.72	58.08	84.91	0.57	0.90	0.55	0.91	0.55	0.47
Apo-Holo dataset defined by iRMSD (native: original and all with iRMSD ≤ 5 Å overlap and non-native: ten with iRMSD > 5 Å overlap with original complex interface)
iRMSD_Model (native: original and one from iRMSD ≤ 5 Å overlap and non-native: iRMSD > 5 Å overlap with original complex interface; ratio: 1:5)
134	680	0.5		124.44	566.56	113.44	9.56	84.89	0.93	0.83	0.53	0.98	0.67	0.62
134	680	0.55		122.68	578.56	101.44	11.32	86.15	0.92	0.85	0.55	0.98	0.69	0.64
134	680	0.6		120.12	587.6	92.4	13.88	86.94	0.90	0.86	0.57	0.98	0.70	0.64
134	680	0.65		117.28	595.6	84.4	16.72	87.58	0.88	0.88	0.59	0.97	0.70	0.65
134	680	0.7		114.32	606.12	73.88	19.68	88.51	0.85	0.89	0.61	0.97	0.71	0.66
134	680	0.75		110.6	617.96	62.04	23.4	89.50	0.83	0.91	0.64	0.96	0.72	0.67
134	680	0.8		104.72	628.36	51.64	29.28	90.06	0.78	0.92	0.67	0.96	0.72	0.67
134	680	0.85		97.88	637.04	42.96	36.12	90.29	0.73	0.94	0.70	0.95	0.71	0.66
134	680	0.9		87.84	648.8	31.2	46.16	90.50	0.66	0.95	0.74	0.93	0.70	0.64
134	680	0.95		69.96	664.28	15.72	64.04	90.20	0.52	0.98	0.82	0.91	0.64	0.60

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Table 2 Benchmarking results for Apo-Holo datasets using the Hetero FNAT and iRMSD models.

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