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. Author manuscript; available in PMC: 2018 Jul 15.
Published in final edited form as: J Chem Theory Comput. 2017 Aug 4;13(9):4253–4269. doi: 10.1021/acs.jctc.7b00359

Table 3.

Error statistics between the computed and experimental binding free energy and binding enthalpy for each force field combination.

Metrics Q4RG-TIP3P Q4RG-TIP4Pew Q4RG-SPC Q4RG-OPC Q4RG-OPC-jc Q4RG-OPC-phos Q4RG-OPC-jcphos Q4BG-TIP3P BGRG-TIP3P BGBG-TIP3P
Binding Free Energy
Slope   1.02 (0.18)   1.03 0.16 0.98 (0.18)   0.90 (0.12)   0.93 (0.14)   0.97 (0.15)   0.86 (0.14)   1.12 (0.17)   0.71 (0.12)   0.74 (0.10)
Intercept −1.31 (0.61) −1.25 0.53 −1.24 (0.63) −0.82 (0.43) −0.74 (0.49) −0.35 (0.52) −0.67 (0.49) −0.96 (0.57) −0.40 (0.40) −0.29 (0.33)
R2   0.47 (0.09)   0.54 0.09   0.44 (0.09)   0.57 (0.08)   0.56 (0.08)   0.53 (0.08)   0.46 (0.10)   0.52 (0.08)   0.52 (0.11) 0.60 (0.09)
Kendall’s τ   0.48 (0.07)   0.52 0.07   0.46 (0.08)   0.55 (0.06)   0.55 (0.07)   0.53 (0.07)   0.46 (0.08)   0.51 (0.07)   0.53 (0.08) 0.57 (0.06)
RMSE   1.80 (0.13)   1.69 0.12   1.67 (0.13)   0.97 (0.09)   1.03 (0.09)   1.00 (0.08)   1.03 (0.09)   1.73 (0.13)   0.92 (0.08) 0.85 (0.08)
MSE −1.38 (0.18) −1.36 0.15 −1.19 (0.18) −0.52 (0.13) −0.53 (0.14) −0.26 (0.15) −0.25 (0.15) −1.30 (0.18)   0.48 (0.12)   0.50 (0.11)
MUE   1.53 (0.15)   1.45 0.13   1.43 (0.13)   0.80 (0.09)   0.87 (0.09)   0.85 (0.08)   0.87 (0.09)   1.51 (0.13)   0.79 (0.07) 0.73 (0.07)
Binding Enthalpy
Slope   0.95 (0.11)   0.95 (0.08) 0.96 (0.12)   0.93 (0.08)   0.93 (0.08)   0.68 (0.07)   0.64 (0.06)   0.94 (0.11)   0.70 (0.16)   0.80 (0.18)
Intercept −1.80 (0.34) 0.10 (0.26) −0.35 (0.36)   2.48 (0.25)   2.22 (0.25)   2.99 (0.21)   2.95 (0.19) −1.78 (0.34)   1.26 (0.53)   1.36 (0.61)
R2   0.68 (0.08) 0.77 (0.06)   0.68 (0.07)   0.71 (0.08)   0.75 (0.07)   0.71 (0.07)   0.70 (0.08)   0.64 (0.08)   0.30 (0.11)   0.39 (0.12)
Kendall’s τ   0.62 (0.06) 0.69 (0.06)   0.62 (0.06)   0.64 (0.07)   0.65 (0.06)   0.61 (0.06)   0.58 (0.08)   0.62 (0.07)   0.44 (0.09)   0.49 (0.08)
RMSE   2.03 (0.17) 0.92 (0.09)   1.17 (0.12)   2.83 (0.16)   2.55 (0.14)   3.89 (0.14)   3.97 (0.14)   2.04 (0.18)   2.78 (0.31)   2.55 (0.24)
MSE −1.69 (0.17) 0.21 (0.14) −0.25 (0.18)   2.64 (0.16)   2.38 (0.14)   3.77 (0.14)   3.85 (0.15) −1.65 (0.19)   1.99 (0.30)   1.84 (0.27)
MUE   1.73 (0.16) 0.77 (0.08)   0.95 (0.11)   2.64 (0.16)   2.38 (0.14)   3.77 (0.14)   3.85 (0.15)   1.72 (0.17)   2.25 (0.26)   2.13 (0.22)

All metrics were computed via sampling with replacement using 100,000 bootstrap cycles. The mean value of the bootstrap distribution is listed along with the standard error of the mean, in parentheses. Linear regressions were of the “y = mx + b” form and did not force the fit through the origin. R2 is the coefficient of determination. RMSE is the root-mean-square error. MSE is the mean signed error. MUE is the mean unsigned error.