Table 2.
Summary of performance metrics for FEP and mm-GB/SA
| Category | Methodology | RMSE (kcal/mol) | R2 | p |
|---|---|---|---|---|
| Non-buried | FEP | 1.23 [1.07–1.38] (1.22) | 0.50 [0.36–0.62] (0.53) | < 0.001 |
| Non-buried | mm-GB/SA | 1.50 [1.22–1.76] (1.50) | 0.18 [0.06–0.33] (0.23) | < 0.001 |
| Buried | FEP | 1.79 [1.41–2.11] (1.95) | 0.52 [0.31–0.71] (0.40) | < 0.001 |
| Buried | mm-GB/SA | 2.80 [2.33–3.28] (2.44) | 0.14 [0.0–0.41] (0.05) | 0.014 |
| All | FEP | 1.41 [1.26–1.59] (1.40) | 0.61 [0.5–0.71] (0.58) | < 0.001 |
| All | mm-GB/SA | 1.97 [1.71–2.21] (1.74) | 0.17 [0.06–0.31] (0.23) | < 0.001 |
Error ranges for metrics (square brackets) are estimated based on a bootstrapping analysis using a 95% confidence interval. Values in parentheses show the result if the cases where acids are modeled entirely or partially, as protonated are excluded.