Table I.

RosettaLigand Energy Scores and X-Scores for Rigid Bound, Rigid Unbound, and Flexible BP-Dock Docking for Unbound Structures with Available Experimental Data

				RosettaLigand score (kcal/mol)			X-Score (kcal/mol)
	PDB code			rigid		BP-Dock	rigid		BP-Dock
protein	bound	unbound	chain length	bound	unbound	unbound	bound	unbound	unbound	Exp_ ΔG
HIV-1 protease	1HBV	2PC0	198	–357.51	–558.70	–390.74	–10.28	–8.78	–9.23	–8.68
	1HEG	2PC0	198	–64.8	–563.82	–402.30	–10.56	–8.19	–8.86	–10.38
	1HIH	2PC0	198	–491.08	–569.36	–397.08	–11.1	–9.33	–10.08	–10.97
	1HIV	2PC0	198	–462.25	–555.32	–393.39	–12.2	–9.13	–10.08	–12.64
	1HPS	2PC0	198	–394.35	–586.28	–416.19	–16.65	–12.55	–14.31	–12.66
	1HTE	2PC0	198	–210.93	–559.65	–383.46	–9.06	–8.36	–8.38	–7.69
	1HTF	2PC0	198	–394.32	–568.62	–402.59	–14.05	–11.04	–11.68	–11.04
	1HTG	2PC0	198	–528.38	–582.81	–413.38	–19.05	–14.77	–14.39	–13.20
	1HVI	2PC0	198	–513.57	–564.07	–401.71	–12.22	–9.85	–10.69	–13.74
	1HVJ	2PC0	198	–496.71	–563.75	–399.83	–12	–10.09	–10.86	–14.26
	1HVK	2PC0	198	–518.85	–568.48	–399.62	–12.53	–9.26	–11.09	–13.79
	1HVL	2PC0	198	–490.64	–565.61	–401.29	–12	–9.98	–10.89	–12.27
	1HVS	2PC0	198	–434.77	–559.28	–408.65	–11.57	–9.84	–10.39	–13.81
	1SBG	2PC0	198	–368.53	–568.57	–405.08	–11.04	–9.14	–9.90	–10.38
	4HVP	2PC0	198	–290.75	–567.84	–381.94	–10.88	–8.77	–9.43	–8.33
	4PHV	2PC0	198	–476.11	–599.01	–432.82	–21.58	–17.60	–18.41	–12.56
	5HVP	2PC0	198	–418.5	–563.39	–398.59	–10.62	–8.62	–8.64	–10.50
	9HVP	2PC0	198	–237.85	–565.45	–403.47	–12.23	–9.73	–10.20	–11.38
	1A30	2PC0	198	–517.82	–538.30	–372.12	–7.48	–6.09	–6.45	–5.77
	1KZK	2PC0	198	–572.92	–545.99	–394.12	–11.78	–9.22	–10.70	–13.94
carbonic anhydrase II	1OQ5	2ILI	259	–715.26	–756.01	–773.92	–8.52	–8.47	–8.49	–10.29
	1AVN	2ILI	259	–592.57	–751.43	–701.87	–5.79	–5.47	–5.4	–2.88
	1CIL	2ILI	259	–721.24	–752.23	–767.82	–7.51	–7.49	–7.8	–12.94
	1CIM	2ILI	259	–685.56	–752.41	–765.94	–7.23	–7.23	–7.34	–12.1
	1CIN	2ILI	259	–700.59	–752.19	–769.06	–7.24	–7.29	–7.23	–11.97
	1CNW	2ILI	259	–623.88	–758.62	–773.11	–6.24	–6.56	–6.56	–10.6
	1CNX	2ILI	259	–628.09	–759.78	–773.72	–6.67	–6.87	–6.93	–10.11
	1CNY	2ILI	259	–559.46	–758.64	–773.63	–6.63	–6.75	–6.8	–10.78
	1OKL	2ILI	259	–755.5	–756.12	–772.95	–7.8	–7.89	–7.84	–12.39
alcohol dehydrogenase	1ADB	8ADH	374	–716.52	–536.87	–1009	–10.47	–8.3	–8.88	–11.45
	1ADC	8ADH	374	–635.01	–539.07	–997.2	–10.41	–8.72	–8.7	–6.42
	1ADF	8ADH	374	–664.17	–535.33	–997.55	–8.16	–8.38	–7.65	–6.24
	1BTO	8ADH	374	–999	–454.08	–962.59	–6.66	–6.4	–6.47	–8.93
	1HLD	8ADH	374	–1001.88	–552.66	–1009.89	–13.33	–10.93	–10.67	–7.58
	1LDE	8ADH	374	–952.57	–536.52	–1005.22	–11.87	–9.52	–9.79	–9.41
	1LDY	8ADH	374	–930.53	–540.04	–1008.14	–12.28	–10.12	–10.03	–11.06
	3BTO	8ADH	374	–1088.23	–546.46	–1006.28	–12.31	–9.89	–9.95	–8.43
alpha-thrombin	1A4W	1C5L	274	–572.9	–791.4	–787.2	–9.43	–8.92	–8.8	–8.13
	1AE8	1C5L	298	–758.2	–790.99	–784.3	–8.42	–8.19	–8.12	–8.99
	1BMM	1C5L	295	–445.95	–796.63	–791.14	–9.15	–9.07	–9.09	–9.75
	1BMN	1C5L	292	–513.89	–792.21	–789.85	–9.66	–9.3	–9.44	–11.58
	1D3D	1C5L	290	–626.78	–794.97	–789.76	–10.16	–9.89	–9.23	–3.27
	1D3P	1C5L	290	–612.8	–796.24	–790.58	–9.43	–9.5	–8.42	–2.93
	1D4P	1C5L	290	–605.2	–796.04	–791.08	–9.64	–9.93	–9.2	–2.28
	1DWB	1C5L	298	–798.4	–783.67	–777.29	–6.7	–6.63	–6.61	–3.98
	1DWC	1C5L	298	–800.78	–789.23	–784.77	–8.82	–8.76	–8.55	–10.6
	1DWD	1C5L	298	–811.38	–797.11	–791.32	–10.22	–10.04	–9.83	–11.57
	1HDT	1C5L	303	–217.53	–795.04	–789.04	–9.66	–9.59	–9.52	–10.66
	1UVS	1C5L	268	–603.35	–788.95	–782.21	–8.74	–8.84	–8.62	–7.41
	1OYT	1C5L	306	–825.83	–792.24	–791.47	–9.23	–9.11	–8.94	–9.71
cytochrome C peroxidase	1AC4	1CCP	291	–753.91	–887.07	–897.53	–5.3	–5.29	–5.27	–3.85
	1AC8	1CCP	291	–790.67	–889.01	–899.96	–6.42	–6.28	–6.29	–4.78
	1AEB	1CCP	291	–790.68	–889.59	–900.82	–5.8	–5.7	–5.69	–4.81
	1AED	1CCP	291	–788.54	–886.36	–897.54	–6.14	–6.03	–6.04	–5.86
	1AEE	1CCP	291	–803.13	–893.8	–904.99	–5.49	–5.83	–5.33	–3.96
	1AEF	1CCP	291	–792.96	–893.39	–914.1	–6.57	–6.21	–6.62	–6
	1AEG	1CCP	291	–795.32	–893.45	–904.04	–6.26	–6.11	–6.09	–5.99
	1AEH	1CCP	291	–793.03	–897.21	–902.31	–6.23	–6.01	–6.02	–4.96
	1AEJ	1CCP	291	–790.57	–891.97	–902.97	–6.07	–6	–5.98	–5.21
	1AEK	1CCP	291	–793.62	–891.75	–902.36	–6.76	–6.64	–6.65	–4.92
	1AEM	1CCP	291	–795.62	–894.37	–905.32	–6.48	–6.4	–6.4	–4.92
	1AEN	1CCP	291	–753.99	–887.28	–898.04	–6.73	–6.06	–6.74	–7.07
	1AEO	1CCP	291	–764.09	–894.73	–904.55	–6.47	–6.36	–6.34	–5.02
	1AEQ	1CCP	291	–790.59	–891.23	–901.78	–6.31	–6.26	–6.26	–4.73
	1AES	1CCP	291	–777.02	–890.29	–900.74	–5.69	–5.59	–5.58	–4.33
	1AET	1CCP	291	–808.57	–890.68	–900.81	–5.78	–5.76	–5.73	–5.82
	1AEU	1CCP	291	–756.73	–891.24	–901.34	–5.92	–6	–6	–5.94
	1AEV	1CCP	291	–783.98	–891.28	–902.13	–6.44	–5.85	–5.85	–6.06