Table 3.

The correlation between the experimental and the calculated binding free energies using three different lengths of MD simulations^a

		r0.2~0.6ns	r0.2~1ns	r0.2~2ns	r0.2~3ns	r0.2~4ns	r0.2~5ns	r1~3ns	r1~5ns	r2~5ns	r3~5ns	sdb
α-thrombin	εin=1	0.60	0.58	0.54	0.52	0.50	0.49	0.49	0.47	0.46	0.45	0.050
	εin =2	0.81	0.80	0.77	0.73	0.72	0.71	0.70	0.69	0.68	0.68	0.048
	εin =4	0.91	0.90	0.87	0.85	0.84	0.83	0.82	0.81	0.80	0.80	0.039
avidin	εin =1	0.93	0.95	0.92	0.86	0.87	0.89	0.80	0.87	0.87	0.92	0.044
	εin =2	0.78	0.80	0.77	0.74	0.73	0.74	0.71	0.73	0.73	0.75	0.027
	εin =4	0.64	0.66	0.66	0.63	0.62	0.63	0.62	0.62	0.61	0.62	0.017
cytochrome C peroxidase	εin =1	0.07	0.20	0.30	0.27	0.25	0.19	0.26	0.17	0.12	0.08	0.081
	εin =2	−0.10	−0.01	0.08	0.06	0.05	0.03	0.08	0.04	0.01	0.01	0.053
	εin =4	−0.19	−0.16	−0.13	−0.14	−0.14	−0.13	−0.14	−0.13	−0.13	−0.11	0.022
neuraminidase	εin =1	−0.26	−0.35	−0.42	−0.39	−0.38	−0.42	−0.38	−0.41	−0.39	−0.42	0.048
	εin =2	0.36	0.11	0.06	0.08	0.10	0.04	0.07	0.03	0.04	0.00	0.101
	εin =4	0.78	0.65	0.65	0.62	0.60	0.54	0.58	0.50	0.45	0.42	0.107
P450cam	εin =1	0.49	0.43	0.59	0.56	0.53	0.57	0.59	0.58	0.54	0.57	0.051
	εin =2	0.63	0.59	0.65	0.61	0.60	0.62	0.61	0.62	0.60	0.63	0.018
	εin =4	0.67	0.63	0.65	0.61	0.61	0.62	0.61	0.61	0.59	0.62	0.023
penicillopepsin	εin =1	0.29	0.26	0.25	0.23	0.21	0.21	0.22	0.21	0.19	0.20	0.031
	εin =2	0.37	0.35	0.35	0.34	0.33	0.33	0.33	0.33	0.32	0.32	0.016
	εin =4	0.35	0.34	0.33	0.32	0.32	0.31	0.32	0.31	0.30	0.30	0.016

^aThe entropy term was not included in the total binding free energy for correlation analysis

^bsd represents the standard deviation of the ten correlation coefficients.