Table 2.

Pairwise comparison of the top-ranked predicted targets across different methodologies including: AF2, OP1, OP2 and OP3.

Target	AF2	AFM-OP1	AFM-OP2	AFM-OP3	Target	AF2	AFM-OP1	AFM-OP2	AFM-OP3	Target	AF2	AFM-OP1	AFM-OP2	AFM-OP3
	GDT_TS	GDT_TS	GDT_TS	GDT_TS		GDT_TS	GDT_TS	GDT_TS	GDT_TS		GDT_TS	GDT_TS	GDT_TS	GDT_TS
7BRM-D1	83.82	86.24*	81.49	84.69	7RB9-D1	85.59	85.46	85.39	85.12	T1042-D1	61.32	59.78	59.78	60.60
7BXT-D1	93.99	90.38	94.71	90.63	T1024-D0	85.68	87.02	65.73	87.02	T1043-D1	25.51	25.84	25.34	27.70
7C2K-D1	93.70	93.29	91.14	93.48	T1024-D1	90.29	89.90	90.16	89.90	T1045s1-D1	95.62	96.10	96.27	96.59
7EDA-D1	98.36	92.01	90.00	95.07	T1024-D2	91.18	91.30	91.30	91.79	T1045s2-D1	93.83	92.02	92.62	93.37
7EV9-D1	97.00	89.69	90.60	89.69	T1025-D1	98.35	98.15	98.25	98.35	T1046s1-D1	97.57	96.87	97.22	97.92
7KU7-D1	79.63	80.46	83.89*	80.56	T1026-D1	92.64	92.81	92.98	92.47	T1046s2-D1	98.76	98.58	98.40	98.76
7KZZ-D1	71.90	75.89	78.63*	75.89	T1028-D1	92.98	93.15	92.38	93.15	T1047s1-D1	47.87	46.68	46.45	47.99
7L1K-D1	97.83	97.83	97.67	97.83	T1029-D1	46.20	46.20	45.40	46.20	T1047s2-D1	89.12	88.61	87.08	87.58
7L6U-D1	91.35	90.22	86.38	90.22	T1030-D0	53.48	68.13*	67.12	62.64	T1047s2-D3	50.43	50.22	49.78	50.22
7LC6-D1	97.49	97.31	97.27	97.18	T1030-D1	71.10	68.34	69.64	70.94	T1049-D1	93.28	92.91	92.72	92.91
7LCI-D1	67.83	67.70	61.87	69.54*	T1030-D2	89.50	85.92	82.14	85.29	T1053-D0	88.72	87.76	88.24	88.28
7LS5-D1	96.52	96.31	95.80	96.21	T1031-D1	94.47	94.47	90.00	94.74	T1053-D1	89.01	89.01	89.26	89.26
7LSX-D1	94.72	93.80	93.90	94.92	T1032-D1	65.59	65.29	65.00	64.85	T1053-D2	84.65	82.46	82.31	85.96
7LV9-D1	73.47	69.64	57.40	69.64	T1033-D1	52.75	42.00	50.00	46.00	T1054-D1	89.34	88.99	88.46	88.99
7LVR-D1	94.29	94.12	94.00	94.29	T1034-D1	95.51	95.19	95.35	95.35	T1055-D1	87.91	88.73	87.91	88.73
7LX5-D1	93.91	93.66	92.64	94.04	T1035-D1	87.75	88.24	87.01	88.24	T1056-D1	97.48	95.71	95.41	96.01
7M7B-D1	90.12	90.36	89.41	90.36	T1036s1-D1	83.17	74.80	63.20	74.80	T1065s1-D1	92.86	93.07	93.91	93.07
7M9C-D1	88.28	86.92	87.69	87.98	T1037-D1	84.71	84.03	86.32*	86.08	T1065s2-D1	97.96	98.47	98.21	98.47
7MBY-D1	90.96	92.06	91.18	91.91	T1038-D0	86.84	85.13	41.84	87.24	T1074-D1	93.18	93.37	91.67	92.42
7ME0-D1	99.28	99.28	96.55	99.28	T1038-D1	85.53	81.36	82.89	86.40	T1076-D1	98.98	99.12	99.07	99.12
7MJS-D1	88.53	88.16	88.35	88.53	T1038-D2	91.78	90.79	90.46	91.12	T1078-D1	94.96	94.96	94.57	94.38
7MLZ-D1	82.49	83.12	82.36	83.12	T1039-D1	85.25	83.70	80.59	82.92	T1082-D1	91.67	90.33	90.33	90.33
7MSW-D1	45.01	44.58	41.94	46.15	T1040-D1	56.54	55.96	55.58	57.12	T1090-D1	89.53	89.53	88.87	89.79
7N8I-D1	98.83	98.83	98.83	99.07	T1041-D1	84.71	85.54	85.12	85.12	T1099-D1	79.35	80.76	82.16	80.62

Results in bold represent pair-to-pair models obtained with either AlphaMod procedure with a GDT_TS score higher than the one obtained by AF2 alone. Results with * represent, for each target, a notable quality increase in terms of GDT_TS score. Results in italic represent pair-to-pair models obtained with either AlphaMod procedure with a GDT_TS score equal to those obtained by AF2 alone.