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ResearchFormerly WizWand

Protein-Ligand Binding Affinity Prediction on PDBbind

1.263RMSEPAMNet
1.246521.357761.4691.58024Nov 19, 2023Apr 17, 2024Sep 14, 2024Feb 11, 2025Jul 11, 2025Dec 8, 2025May 8, 2026
Updated 5mo ago

Evaluation results

MethodLinks
PAMNetModel Category=Ours2023.111.2630.9871.2610.815
PAMNetBatch Size=32, Hidden Dim.=128, Initial Learning Rate=0.001, Number of Layers=3, Max. Number of Epochs=1002023.111.2630.9871.2610.815
SIGNModel Category=GNN-based2023.111.3161.0271.3120.797
SIGN2023.111.3161.0271.3120.797
DTSemNet STEHeight=2, Number of features (Nf)=2052, Number of training samples (Ns)=90132026.051.33———
DTSemNet Top-kHeight=2, Number of features (Nf)=2052, Number of training samples (Ns)=90132026.051.34———
DGT-LinearHeight=2, Number of features (Nf)=2052, Number of training samples (Ns)=90132026.051.34———
OnionNetModel Category=CNN-based2023.111.4071.0781.3910.768
CMPNNModel Category=GNN-based2023.111.4081.1171.3990.765
RF-ScoreModel Category=ML-based2023.111.4461.1611.3350.789
DimeNetModel Category=GNN-based2023.111.4531.1381.4340.752
MATModel Category=GNN-based2023.111.4571.1541.4450.747
GNN-DTIModel Category=GNN-based2023.111.4921.1921.4710.736
D-MPNNModel Category=GNN-based2023.111.4931.1881.4890.729
CARTNumber of features (Nf)=2052, Number of training samples (Ns)=90132026.051.55———
SVRModel Category=ML-based2023.111.5551.2641.4930.727
GraphDTAModel Category=GNN-based2023.111.5621.1911.5580.697
SGCNModel Category=GNN-based2023.111.5831.251.5820.686
PafnucyModel Category=CNN-based2023.111.5851.2841.5630.695
LRModel Category=ML-based2023.111.6751.3581.6120.671