Protein-Ligand Binding Affinity Prediction on PDBbind
1.263RMSEPAMNet
Evaluation Results
| Method | Links | ||||
|---|---|---|---|---|---|
| PAMNetModel Category=Ours2023.11 | 1.263 | 0.987 | 1.261 | 0.815 | |
| PAMNetBatch Size=32, Hidden Dim.=128, Initial Learning Rate=0.001, Number of Layers=3, Max. Number of Epochs=1002023.11 | 1.263 | 0.987 | 1.261 | 0.815 | |
| SIGNModel Category=GNN-based2023.11 | 1.316 | 1.027 | 1.312 | 0.797 | |
| SIGN2023.11 | 1.316 | 1.027 | 1.312 | 0.797 | |
| DTSemNet STEHeight=2, Number of features (Nf)=2052, Number of training samples (Ns)=90132026.05 | 1.33 | — | — | — | |
| DTSemNet Top-kHeight=2, Number of features (Nf)=2052, Number of training samples (Ns)=90132026.05 | 1.34 | — | — | — | |
| DGT-LinearHeight=2, Number of features (Nf)=2052, Number of training samples (Ns)=90132026.05 | 1.34 | — | — | — | |
| OnionNetModel Category=CNN-based2023.11 | 1.407 | 1.078 | 1.391 | 0.768 | |
| CMPNNModel Category=GNN-based2023.11 | 1.408 | 1.117 | 1.399 | 0.765 | |
| RF-ScoreModel Category=ML-based2023.11 | 1.446 | 1.161 | 1.335 | 0.789 | |
| DimeNetModel Category=GNN-based2023.11 | 1.453 | 1.138 | 1.434 | 0.752 | |
| MATModel Category=GNN-based2023.11 | 1.457 | 1.154 | 1.445 | 0.747 | |
| GNN-DTIModel Category=GNN-based2023.11 | 1.492 | 1.192 | 1.471 | 0.736 | |
| D-MPNNModel Category=GNN-based2023.11 | 1.493 | 1.188 | 1.489 | 0.729 | |
| CARTNumber of features (Nf)=2052, Number of training samples (Ns)=90132026.05 | 1.55 | — | — | — | |
| SVRModel Category=ML-based2023.11 | 1.555 | 1.264 | 1.493 | 0.727 | |
| GraphDTAModel Category=GNN-based2023.11 | 1.562 | 1.191 | 1.558 | 0.697 | |
| SGCNModel Category=GNN-based2023.11 | 1.583 | 1.25 | 1.582 | 0.686 | |
| PafnucyModel Category=CNN-based2023.11 | 1.585 | 1.284 | 1.563 | 0.695 | |
| LRModel Category=ML-based2023.11 | 1.675 | 1.358 | 1.612 | 0.671 |