Table 2.
Rescoring Fpocket and ConCavity predictions with PRANK: cross-validation results on CHEN11 dataset and the results of the final prediction model (trained on CHEN11-Fpocket) for all datasets
| Dataset | Top-n [%] | Rescored [%] | All [%] | Δ | %possible* | P | R | MCC |
|---|---|---|---|---|---|---|---|---|
| Fpocket predictions | ||||||||
| CHEN11 (CV)** | 47.9 | 58.8 | 71 | +10.6 | 47.1 | 0.60 | 0.32 | 0.41 |
| CHEN11*** | 47.9 | 67.9 | 71 | +20 | 86.4 | 0.87 | 1.0 | 0.98 |
| ASTEX | 58 | 63.6 | 81.1 | +5.6 | 24.2 | 0.56 | 0.41 | 0.46 |
| DT198 | 37.5 | 56.2 | 80.2 | +18.8 | 43.9 | 0.31 | 0.38 | 0.33 |
| MP210 | 56.6 | 67.7 | 78.8 | +11.1 | 50 | 0.58 | 0.42 | 0.47 |
| B48 | 74.1 | 81.5 | 92.6 | +7.4 | 40 | 0.58 | 0.45 | 0.49 |
| U48 | 53.7 | 77.8 | 88.9 | +24.1 | 68.4 | 0.55 | 0.36 | 0.42 |
| ConCavity predictions | ||||||||
| CHEN11 (CV)** | 47.9 | 50.7 | 52.3 | +2.8 | 63.3 | 0.44 | 0.76 | 0.40 |
| CHEN11*** | 47.9 | 52.3 | 52.3 | +4.4 | 100 | 0.80 | 0.82 | 0.75 |
| ASTEX | 55.2 | 62.9 | 65.7 | +7.7 | 73.3 | 0.60 | 0.55 | 0.46 |
| DT198 | 45.8 | 61.5 | 65.6 | +15.6 | 78.9 | 0.33 | 0.55 | 0.34 |
| MP210 | 57.4 | 66.1 | 68.2 | +8.7 | 80.6 | 0.63 | 0.53 | 0.49 |
| B48 | 66.7 | 77.8 | 81.5 | +11.1 | 75 | 0.61 | 0.53 | 0.47 |
| U48 | 64.8 | 74.1 | 77.8 | +9.3 | 71.4 | 0.58 | 0.46 | 0.43 |
Abbreviations: P precision, R recall, MCC Matthews correlation coefficient.
*percentage of improvement that was theoretically possible to obtain by reordering pockets [ Δ / (All – Top-n)].
**cross-validation results.
***results where the test set was de facto the same as the training set for the Random Forest classifier (included here only for completeness).