Table 2 Performance of the four models trained on crystal and docked poses and tested also on crystal and docked poses (schemes 1 and 2) on the PDBbind v2013 blind benchmark
From: Correcting the impact of docking pose generation error on binding affinity prediction
Model | Training | Test | RMSE | SD | Rp | Rs |
|---|---|---|---|---|---|---|
1 (Vina) | Crystal | Crystal | 2.30 | 1.81 | 0.406 | 0.414 |
2 (MLR::Vina) | Crystal | Crystal | 1.67 | 1.67 | 0.535 | 0.521 |
3 (RF::Vina) | Crystal | Crystal | 1.54 | 1.54 | 0.629 | 0.593 |
4 (RF::VinaElem) | Crystal | Crystal | 1.43 | 1.43 | 0.689 | 0.662 |
1 (Vina) | Crystal | Docked | 1.87 | 1.78 | 0.437 | 0.432 |
2 (MLR::Vina) | Crystal | Docked | 1.70 | 1.69 | 0.520 | 0.505 |
3 (RF::Vina) | Crystal | Docked | 1.61 | 1.60 | 0.585 | 0.549 |
4 (RF::VinaElem) | Crystal | Docked | 1.49 | 1.49 | 0.656 | 0.633 |
2 (MLR::Vina) | Docked | Crystal | 1.69 | 1.69 | 0.521 | 0.509 |
3 (RF::Vina) | Docked | Crystal | 1.62 | 1.61 | 0.580 | 0.560 |
4 (RF::VinaElem) | Docked | Crystal | 1.48 | 1.47 | 0.669 | 0.650 |
2 (MLR::Vina) | Docked | Docked | 1.68 | 1.68 | 0.524 | 0.509 |
3 (RF::Vina) | Docked | Docked | 1.59 | 1.59 | 0.594 | 0.553 |
4 (RF::VinaElem) | Docked | Docked | 1.47 | 1.48 | 0.665 | 0.643 |