Table 2. Overview of the Results Obtained with ABFE and MMPBSA Calculations, in Terms of Pearson and Spearman Correlation to Experimental Binding Free Energiesa.
| Pearson Correlation | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Test Case No. | Weight | ABFE | W0 | W0e | W10 | W20 | W30 | W40 | W50 |
| 1a | 5.5 | 0.87 [0.73, 0.92] | 0.71 [0.61, 0.76] | 0.73 [0.31, 0.85] | 0.77 [0.62, 0.86] | 0.82 [0.75, 0.86] | 0.83 [0.79, 0.87] | 0.83 [0.79, 0.86] | 0.83 [0.79, 0.86] |
| 1b | 5.5 | 0.78 [0.67, 0.84] | 0.79 [0.75, 0.82] | 0.67 [0.56, 0.76] | 0.89 [0.85, 0.91] | 0.90 [0.86, 0.92] | 0.88 [0.85, 0.91] | 0.87 [0.83, 0.89] | 0.86 [0.83, 0.89] |
| 2 | 14 | 0.75 [0.67, 0.80] | 0.05 [−0.06, 0.17] | 0.63 [0.46, 0.72] | 0.44 [0.32, 0.54] | 0.50 [0.37, 0.60] | 0.10 [−0.05, 0.25] | –0.14 [−0.29, 0.01] | –0.23 [−0.37, −0.08] |
| 3 | 22 | 0.48 [0.41, 0.53] | 0.42 [0.38, 0.46] | 0.43 [0.31, 0.51] | 0.36 [0.30, 0.43] | 0.38 [0.32, 0.44] | 0.39 [0.34, 0.44] | 0.35 [0.30, 0.40] | 0.34 [0.29, 0.39] |
| Weighted Average | 0.64 [0.56, 0.69] | 0.39 [0.32, 0.45] | 0.55 [0.39, 0.64] | 0.50 [0.41, 0.57] | 0.53 [0.45, 0.59] | 0.42 [0.34, 0.49] | 0.32 [0.24, 0.39] | 0.29 [0.21, 0.36] | |
| Spearman Correlation | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Test Case No. | Weight | ABFE | W0 | W0e | W10 | W20 | W30 | W40 | W50 |
| 1a | 5.5 | 0.85 [0.69, 0.94] | 0.72 [0.62, 0.83] | 0.61 [0.17, 0.82] | 0.57 [0.50, 0.82] | 0.77 [0.67, 0.85] | 0.83 [0.74, 0.86] | 0.83 [0.74, 0.85] | 0.79 [0.73, 0.85] |
| 1b | 5.5 | 0.78 [0.55, 0.85] | 0.79 [0.72, 0.85] | 0.75 [0.47, 0.82] | 0.79 [0.75, 0.85] | 0.85 [0.78, 0.89] | 0.85 [0.77, 0.87] | 0.83 [0.75, 0.85] | 0.83 [0.75, 0.85] |
| 2 | 14 | 0.78 [0.64, 0.85] | –0.05 [−0.15, 0.20] | 0.57 [0.38, 0.74] | 0.31 [0.24, 0.53] | 0.46 [0.25, 0.60] | 0.11 [−0.06, 0.36] | 0.02 [−0.19, 0.23] | –0.05 [−0.28, 0.18] |
| 3 | 22 | 0.50 [0.41, 0.62] | 0.41 [0.36, 0.52] | 0.50 [0.35, 0.61] | 0.48 [0.40, 0.59] | 0.48 [0.37, 0.56] | 0.48 [0.40, 0.57] | 0.45 [0.35, 0.53] | 0.41 [0.34, 0.51] |
| Weighted Average | 0.66 [0.53, 0.75] | 0.35 [0.28, 0.50] | 0.56 [0.35, 0.70] | 0.48 [0.40, 0.63] | 0.55 [0.42, 0.64] | 0.45 [0.35, 0.58] | 0.41 [0.28, 0.52] | 0.37 [0.25, 0.49] | |
a
In square brackets are the 95% confidence intervals of the statistics. W0 refers to the single-trajectory MMPBSA protocol that did not include a binding entropy estimate or explicit water molecules; W0e refers to the protocol that included a binding entropy estimate (but no explicit water molecules); W10 to W50 refer to the protocols that included an explicit ligand hydration shell composed of 10 to 50 water molecules (but no binding entropy estimate).