Dual-target drug design on 12,917 Dual-Target Pairs (test)
-9.6P-1 Vina Dock (Avg)REUSE (w/o chemctrl)
Evaluation results
| Method | Links | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| REUSE (w/o chemctrl)Backbone=TargetDiff, Ablation=without chemical control2026.05 | -9.6 | -9.55 | -8.81 | -8.92 | -8.47 | -8.32 | 54.5 | 54.5 | 0.52 | 0.52 | 0.51 | 0.51 | 0.47 | 0.51 | 51.5 | 53.7 | |
| REUSEBackbone=TargetDiff2026.05 | -9.41 | -9.38 | -9.26 | -9.64 | -8.64 | -8.58 | 58.3 | 57.3 | 0.62 | 0.67 | 0.57 | 0.56 | 0.48 | 0.46 | 50.1 | 48.8 | |
| REUSE (w/o balance)Backbone=TargetDiff, Ablation=without balance optimization2026.05 | -9.14 | -9.26 | -9.02 | -9.26 | -8.41 | -8.62 | 55.2 | 50.8 | 0.61 | 0.63 | 0.56 | 0.55 | 0.44 | 0.43 | 48.3 | 47.7 | |
| TargetDiffgeneration_target=P1 only, molecules_per_pair=102024.10 | -8.62 | -8.61 | -6.89 | -7.67 | -6.57 | -7.39 | 29 | 20 | 0.5 | 0.51 | 0.58 | 0.58 | 0.7 | 0.71 | — | — | |
| TargetDiffModel Category=single-target generative baseline2026.05 | -8.61 | -8.65 | -6.96 | -7.45 | -6.43 | -7.21 | 28.6 | 20.1 | 0.52 | 0.53 | 0.56 | 0.57 | 0.71 | 0.71 | 27.4 | 18.6 | |
| DUALDIFFprovided_with_reference_molecules=false, molecules_per_pair=102024.10 | -8.41 | -8.51 | -8.48 | -8.55 | -7.66 | -7.88 | 36.3 | 30.2 | 0.56 | 0.58 | 0.59 | 0.59 | 0.67 | 0.67 | — | — | |
| DualDiffModel Category=dual-target baseline2026.05 | -8.36 | -8.48 | -8.42 | -8.51 | -7.63 | -7.81 | 36.1 | 30.1 | 0.53 | 0.52 | 0.54 | 0.55 | 0.65 | 0.67 | 34.9 | 29.2 | |
| MDRLModel Category=dual-target baseline2026.05 | -8.34 | -8.43 | -8.48 | -8.67 | -7.93 | -8.12 | 37.4 | 31.7 | 0.78 | 0.78 | 0.86 | 0.86 | 0.75 | 0.74 | 37.8 | 30.5 | |
| COMPDIFFprovided_with_reference_molecules=false, molecules_per_pair=102024.10 | -8.32 | -8.42 | -8.37 | -8.47 | -7.5 | -7.78 | 35.9 | 30 | 0.55 | 0.57 | 0.59 | 0.59 | 0.72 | 0.72 | — | — | |
| ComPDIFFModel Category=dual-target baseline2026.05 | -8.25 | -8.34 | -8.29 | -8.41 | -7.45 | -7.73 | 35.5 | 29.8 | 0.54 | 0.53 | 0.54 | 0.55 | 0.72 | 0.72 | 34.2 | 28.7 | |
| LinkerNetprovided_with_reference_molecules=true, molecules_per_pair=102024.10 | -8.2 | -8.37 | -8.13 | -8.38 | -7.17 | -7.72 | 35.7 | 0 | 0.61 | 0.63 | 0.72 | 0.73 | 0.37 | 0.34 | — | — | |
| LinkerNetModel Category=linker-design baseline2026.05 | -8.16 | -8.35 | -8.11 | -8.35 | -7.15 | -7.66 | 35.4 | 0 | 0.59 | 0.61 | 0.71 | 0.71 | 0.35 | 0.33 | 33.8 | 0 | |
| REUSE (w/o search)Backbone=TargetDiff, Ablation=without stage-wise search2026.05 | -8.02 | -8.11 | -7.94 | -8.06 | -7.35 | -7.48 | 31.8 | 26.4 | 0.56 | 0.58 | 0.55 | 0.56 | 0.45 | 0.44 | 30.9 | 25.7 | |
| Referencetype=Reference molecules2024.10 | -7.6 | -7.8 | -6.02 | -7.3 | -5.46 | -7.09 | — | — | 0.53 | 0.54 | 0.74 | 0.77 | — | — | — | — | |
| ReferenceType=Benchmark-associated reference ligands2026.05 | -7.6 | -7.8 | -6.02 | -7.3 | -5.46 | -7.09 | — | — | 0.53 | 0.54 | 0.74 | 0.77 | — | — | — | — | |
| DiffLinkerprovided_with_reference_molecules=true, molecules_per_pair=102024.10 | -7.05 | -7.87 | -7.27 | -7.92 | -5.87 | -7.18 | 24.6 | 0 | 0.43 | 0.42 | 0.3 | 0.29 | 0.52 | 0.54 | — | — | |
| DiffLinkerModel Category=linker-design baseline2026.05 | -7.01 | -7.75 | -7.24 | -7.87 | -5.83 | -7.11 | 24.5 | 0 | 0.44 | 0.45 | 0.31 | 0.27 | 0.51 | 0.52 | 22.8 | 0 | |
| Pocket2Molgeneration_target=P1 only, molecules_per_pair=102024.10 | -4.82 | -4.76 | -4.63 | -4.64 | -4.4 | -4.42 | 0.2 | 0 | 0.49 | 0.48 | 0.88 | 0.9 | 0.82 | 0.83 | — | — | |
| Pocket2MolModel Category=single-target generative baseline2026.05 | -4.71 | -4.66 | -4.64 | -4.65 | -4.42 | -4.41 | 0.2 | 0 | 0.48 | 0.49 | 0.86 | 0.88 | 0.83 | 0.81 | 0.1 | 0 |