Table 5.
Absolute error metrics of binding affinity predictions for the CBClip datasets
| Method | RMSE | R2 | m | τ |
|---|---|---|---|---|
| Null1a | 6.9 (6.9 ± 0.7) | – | – | – |
| Null2b | 2.2 (2.4 ± 0.5) | 0.2 (0.2 ± 0.2) | 0.4 (0.4 ± 0.3) | 0.4 (0.3 ± 0.2) |
| BAR-ab initio | 4.0 (4.0 ± 0.8) | 0.0 (0.1 ± 0.1) | −0.1 (−0.1 ± 0.4) | −0.2 (−0.1 ± 0.2) |
| BAR-dock | 4.7 (4.9 ± 1.0) | 0.1 (0.1 ± 0.1) | −0.4 (−0.4 ± 0.6) | −0.2 (−0.2 ± 0.2) |
| TI-ab initio | 4.7 (4.8 ± 0.8) | 0.2 (0.2 ± 0.2) | −0.6 (−0.6 ± 0.5) | −0.2 (−0.2 ± 0.3) |
| TI-dock | 3.4 (3.6 ± 0.7) | 0.0 (0.1 ± 0.1) | −0.1 (−0.1 ± 0.5) | −0.2 (−0.1 ± 0.2) |
| TI/BAR | 4.0 (4.0 ± 0.9) | 0.0 (0.1 ± 0.1) | −0.1 (−0.1 ± 0.4) | −0.2 (−0.1 ± 0.2) |
| BEDAM | 4.8 (4.6 ± 1.3) | 0.4 (0.5 ± 0.2) | 1.7 (1.8 ± 0.8) | 0.4 (0.4 ± 0.2) |
| MovTyp-1c | 3.5 (3.5 ± 0.7) | 0.0 (0.1 ± 0.1) | 0.0 (0.0 ± 0.3) | 0.0 (0.0 ± 0.3) |
| MovTyp-2c | 4.2 (4.1 ± 0.8) | 0.0 (0.1 ± 0.1) | 0.0 (0.0 ± 0.5) | 0.0 (0.0 ± 0.3) |
| SOMD-1 | 6.4 (6.4 ± 0.9) | 0.8 (0.7 ± 0.2) | 2.7 (2.7 ± 0.5) | 0.7 (0.6 ± 0.1) |
| SOMD-2 | 6.3 (6.3 ± 0.9) | 0.8 (0.7 ± 0.2) | 2.7 (2.7 ± 0.5) | 0.7 (0.6 ± 0.1) |
| SOMD-3 | 5.7 (5.7 ± 0.7) | 0.8 (0.7 ± 0.2) | 2.7 (2.7 ± 0.5) | 0.7 (0.6 ± 0.2) |
| SOMD-4 | 18.4 (17.7 ± 5.3) | 0.5 (0.5 ± 0.3) | 5.6 (5.6 ± 2.4) | 0.5 (0.5 ± 0.3) |
The values before the parentheses are raw error metrics computed from the original data. The mean values and uncertainties inside the parentheses were obtained through resampling the original data using replacement. The absolute error metrics RMSE, R2, m and τ are provided
Null1 model with a constant value 0.0 and no computational uncertainties were assigned to guests
Null2 model based on the linear regression equation ΔG = −0.25 × number of heavy atoms −1.81 kcal/mol (based on SAMPL3 Host1 data); SEM was set to 1.0 kcal/mol
Computational uncertainties were not reported. Results were adversely affected by bond order issues in the provided SD files of free guests [40]