| Methods | RMSE | MAE | R | SD | CI |
| GraphPLA GAT-GCN | 1.388 | 1.118 | 0.795 | 1.345 | 0.796 |
| GraphPLA GCN | 1.392 | 1.121 | 0.795 | 1.351 | 0.792 |
| GraphPLA GAT | 1.396 | 1.126 | 0.796 | 1.348 | 0.789 |
| DeepDTA | 1.443 | 1.148 | 0.749 | 1.445 | 0.771 |
| Pafnucy | 1.418 | 1.129 | 0.775 | 1.375 | 0.789 |
| TopologyNet | 3.713 | 3.151 | 0.173 | 2.142 | 0.555 |