. Author manuscript; available in PMC: 2013 May 25.

Published in final edited form as: J Chem Inf Model. 2012 Apr 24;52(5):1199–1212. doi: 10.1021/ci300064d

Table 4.

Performance of two MM-PBSA protocols in binding free energy calculations^*.

Protein Systems	#Ligand	MM-PBSA-NMA			MM-PBSA-WSAS

		AUE	RMSE	R²	AUE	RMSE	R²
α-thrombin	7	1.40	1.57	0.64	1.21	1.42	0.70
avidin	7	1.62	1.92	0.87	2.43	2.58	0.77
cytochrome C peroxidase	18	0.66	0.77	0.09	0.65	0.76	0.11
neuraminidase	8	1.75	1.92	0.46	1.87	2.09	0.36
P450cam	9	0.54	0.64	0.46	0.66	0.75	0.25
Penicillopepsin^**	4	0.89	0.94	0.03	0.66	0.86	0.18
Mean		1.14	1.29	0.42	1.25	1.41	0.40

AUE and RMSE are in kcal/mol.

^**

Three ligands, f5, f6 and f7 in the paper of Hou et al. (Ref. 19) were eliminated because of apparently wrong molecular structures.