. Author manuscript; available in PMC: 2011 Mar 9.

Published in final edited form as: J Chem Theory Comput. 2010 Mar 9;6(3):607–624. doi: 10.1021/ct900460m

Table 2.

Comparison of explicit TIP3P ΔG_pol for deca-alanine with 3D-RISM-KH, Poisson Equation (PE) and generalized Born (GB). Conformations are as in Roe et al.⁶¹ (alpha:α-helix, PP2:polyproline II, left:left-hand helix and hairpin:β-hairpin). Units are kcal/mol and errors are one standard deviation from the mean.

	TIP3P^a	3D-RISM^b		PE^a	GBHCT^a	GBOBC^a	GBNeck^a

		cTIP3P	PR-TIP3P
(a) ΔG_pol

alpha	-44.08±0.04	-44.91±1.27	-55.79±0.93	-47.97±0.77	-51.69±1.21	-49.38±1.21	-43.26±0.90
PP2	-76.39±0.15	-76.82±1.31	-93.60±1.07	-78.05±0.91	-77.35±1.05	-78.07±1.09	-77.59±1.02
left	-51.30±0.12	-51.60±1.22	-61.81±1.03	-54.85±0.90	-55.05±1.08	-52.67±1.10	-48.19±0.91
hairpin	-54.16±0.25	-56.00±1.17	-69.36±1.31	-57.28±1.13	-57.48±1.45	-56.03±1.47	-52.85±1.29

(b) ΔΔG_pol

PP2-alpha	-32.31	-31.91	-37.81	-30.07	-25.67	-28.69	-34.33
PP2-left	-25.09	-25.22	-31.79	-23.19	-22.31	-25.40	-29.40
PP2-hairpin	-22.23	-20.82	-24.24	-20.77	-19.87	-22.03	-24.73
alpha-left	7.22	6.69	6.02	6.88	3.36	3.29	4.93
alpha-hairpin	10.08	11.09	13.57	9.31	5.80	6.66	9.60
left-hairpin	2.86	4.40	7.55	2.43	2.43	3.37	4.67

(c) ΔΔG_pol Root-Mean-Square Deviations

overall		0.99	4.37	1.39	3.89	2.60	2.51
PP2		0.85	5.14	1.89	4.37	2.10	3.11
non-PP2		1.11	3.45	0.55	3.34	3.02	1.71
hairpin		1.34	3.57	1.53	2.83	2.00	1.80
non-hairpin		0.39	5.05	1.58	4.72	3.09	3.05

From Roe et al.⁶¹

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