. Author manuscript; available in PMC: 2010 Oct 29.

Published in final edited form as: J Phys Chem B. 2009 Oct 29;113(43):14343–14354. doi: 10.1021/jp907375b

Table V.

RMSD of the best docking pose identified by different energy models. The simulations were run by using the GBMV model.^*

System		PTP- Peptide	YopH- Peptide	PTK- Peptide	IGF- Peptide	PKA- Peptide	CDK- Peptide
Energy and solvation model		PTP- Peptide	YopH- Peptide	PTK- Peptide	IGF- Peptide	PKA- Peptide	CDK- Peptide
I	GBMV	2.72	9.69	10.95	2.10	3.09	3.96
	GBMV	1.72	9.41	10.48	1.70	2.30	3.13
	ε(r)=4r	1.98	1.21	2.42	1.19	1.62	1.47
	ε(r)=4r	1.10	0.70	1.60	0.88	1.23	0.70
II	GBMV	3.79	9.63	10.89	2.37	8.14	5.76
	GBMV	2.26	9.55	10.37	1.91	7.53	4.54
	ε(r)=4r	2.36	1.73	1.76	2.04	2.66	3.17
	ε(r)=4r	1.49	0.78	1.69	1.39	2.38	2.84
III	GBMV	3.79	9.62	5.99	2.37	7.93	5.66
	GBMV	2.26	9.53	5.56	1.92	7.60	4.77
	ε(r)=4r	2.44	1.81	1.89	2.85	2.66	5.68
	ε(r)=4r	1.43	1.16	1.60	2.23	2.36	4.79

See footnote of Table IV.