Structure-based drug design on CrossDocked 2020
4.96Avg LipinskiDePPA
Evaluation results
| Method | Links | |||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| DePPA2026.05 | 4.96 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | |
| Pocket2Mol2026.05 | 4.88 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | |
| PROBEModel Category=LLM-agent optimization, Initial Generator=TAGMol, LLM Backbone=GPT-4o-mini, DMTA iterations=52026.05 | 4.85 | -9.168 | — | 0.702 | 0.696 | 48.43 | 62.18 | 55.63 | 2.96 | 365.22 | 4 | — | — | — | — | — | — | — | — | — | — | — | — | |
| PROBEModel Category=LLM-agent optimization, Initial Generator=MolCRAFT, LLM Backbone=GPT-4o-mini, DMTA iterations=52026.05 | 4.85 | -9.203 | — | 0.689 | 0.766 | 63.76 | 79.58 | 52.61 | 2.97 | 359.53 | 2 | — | — | — | — | — | — | — | — | — | — | — | — | |
| Pocket2MolModel Category=De novo 3D-generation2026.05 | 4.83 | -7.245 | — | 0.567 | 0.755 | 22.82 | 70.97 | 29.83 | 1.7 | 243.54 | 15 | — | — | — | — | — | — | — | — | — | — | — | — | |
| MoLLMModel Category=LLM-agent optimization, Initial Generator=TAGMol, LLM Backbone=GPT-4o-mini, DMTA iterations=52026.05 | 4.81 | -8.052 | — | 0.566 | 0.621 | 16.65 | 47.31 | 29.26 | 2.54 | 357.53 | 19 | — | — | — | — | — | — | — | — | — | — | — | — | |
| LIDDIAModel Category=LLM-agent optimization, Initial Generator=TAGMol, LLM Backbone=GPT-4o-mini, DMTA iterations=52026.05 | 4.81 | -7.724 | — | 0.556 | 0.679 | 21.52 | 55.43 | 33.71 | 2.83 | 374.82 | 17 | — | — | — | — | — | — | — | — | — | — | — | — | |
| MOCModel Category=De novo 3D-generation2026.05 | 4.78 | -7.685 | — | 0.559 | 0.647 | 22.6 | 25 | 40.6 | 3.09 | 304.2 | 16 | — | — | — | — | — | — | — | — | — | — | — | — | |
| ARModel Category=De novo 3D-generation2026.05 | 4.76 | -6.613 | — | 0.506 | 0.635 | 5.98 | 64.85 | 20.31 | 0.45 | 247.61 | 27 | — | — | — | — | — | — | — | — | — | — | — | — | |
| AR2026.05 | 4.75 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | |
| CIDDModel Category=LLM-agent optimization, Initial Generator=TAGMol, LLM Backbone=GPT-4o-mini, DMTA iterations=52026.05 | 4.74 | -7.944 | — | 0.641 | 0.665 | 24.53 | 59.19 | 47.79 | 3.01 | 333.51 | 14 | — | — | — | — | — | — | — | — | — | — | — | — | |
| TAGMolModel Category=De novo 3D-generation2026.05 | 4.73 | -7.571 | — | 0.55 | 0.571 | 7.8 | 40 | 31.1 | 1.86 | 337.48 | 25 | — | — | — | — | — | — | — | — | — | — | — | — | |
| IDOLproModel Category=De novo 3D-generation2026.05 | 4.72 | -7.611 | — | 0.548 | 0.568 | 7.6 | 38.2 | 30.1 | 1.81 | 342.72 | 26 | — | — | — | — | — | — | — | — | — | — | — | — | |
| MoLLMModel Category=LLM-agent optimization, Initial Generator=MolCRAFT, LLM Backbone=GPT-4o-mini, DMTA iterations=52026.05 | 4.69 | -8.135 | — | 0.514 | 0.698 | 30.32 | 65.27 | 24.06 | 2.26 | 346.78 | 10 | — | — | — | — | — | — | — | — | — | — | — | — | |
| CIDDModel Category=LLM-agent optimization, Initial Generator=MolCRAFT, LLM Backbone=GPT-4o-mini, DMTA iterations=52026.05 | 4.69 | -7.946 | — | 0.598 | 0.739 | 31.4 | 70.6 | 37.1 | 2.07 | 331.58 | 8 | — | — | — | — | — | — | — | — | — | — | — | — | |
| PROBEModel Category=LLM-agent optimization, Initial Generator=MolJO, LLM Backbone=GPT-4o-mini, DMTA iterations=52026.05 | 4.67 | -9.626 | — | 0.664 | 0.782 | 67.67 | 66.94 | 34.69 | 4.16 | 344.32 | 1 | — | — | — | — | — | — | — | — | — | — | — | — | |
| CIDDModel Category=LLM-agent optimization, Initial Generator=MolJO, LLM Backbone=GPT-4o-mini, DMTA iterations=52026.05 | 4.63 | -8.568 | — | 0.632 | 0.762 | 47.8 | 57.05 | 30.16 | 4.18 | 314.59 | 5 | — | — | — | — | — | — | — | — | — | — | — | — | |
| MolPilotModel Category=De novo 3D-generation2026.05 | 4.6 | -7.818 | — | 0.552 | 0.736 | 30 | 77.5 | 32.3 | 1.8 | 323.97 | 11 | — | — | — | — | — | — | — | — | — | — | — | — | |
| MoLLMModel Category=LLM-agent optimization, Initial Generator=MolJO, LLM Backbone=GPT-4o-mini, DMTA iterations=52026.05 | 4.6 | -8.755 | — | 0.556 | 0.746 | 43.61 | 42.86 | 21.31 | 4.38 | 331.61 | 7 | — | — | — | — | — | — | — | — | — | — | — | — | |
| LIDDIAModel Category=LLM-agent optimization, Initial Generator=MolJO, LLM Backbone=GPT-4o-mini, DMTA iterations=52026.05 | 4.59 | -8.693 | — | 0.567 | 0.765 | 48.44 | 56.93 | 29.65 | 3.79 | 354.36 | 3 | — | — | — | — | — | — | — | — | — | — | — | — | |
| DiffSBDD2026.05 | 4.56 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | |
| MolJOModel Category=De novo 3D-generation2026.05 | 4.55 | -8.663 | — | 0.56 | 0.763 | 46.8 | 41.3 | 14.9 | 4.18 | 308.81 | 6 | — | — | — | — | — | — | — | — | — | — | — | — | |
| IPDiffModel Category=De novo 3D-generation2026.05 | 4.53 | -7.806 | — | 0.521 | 0.593 | 14.5 | 26.3 | 23.5 | 3.46 | 331.6 | 20 | — | — | — | — | — | — | — | — | — | — | — | — | |
| IPDiff2026.05 | 4.52 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | |
| TargetDiff2026.05 | 4.51 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | |
| LIDDIAModel Category=LLM-agent optimization, Initial Generator=MolCRAFT, LLM Backbone=GPT-4o-mini, DMTA iterations=52026.05 | 4.51 | -7.934 | — | 0.524 | 0.712 | 28.25 | 69.22 | 27.14 | 2.27 | 362.73 | 12 | — | — | — | — | — | — | — | — | — | — | — | — | |
| AliDiff2026.05 | 4.48 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | |
| DrugGPSModel Category=De novo 3D-generation2026.05 | 4.45 | -7.295 | — | 0.465 | 0.636 | 13.7 | 56.7 | 26.5 | 1.39 | 328.82 | 21 | — | — | — | — | — | — | — | — | — | — | — | — | |
| TamGenModel Category=De novo 3D-generation2026.05 | 4.44 | -7.476 | — | 0.508 | 0.573 | 8.01 | 24.62 | 30.33 | 4.16 | 326.46 | 24 | — | — | — | — | — | — | — | — | — | — | — | — | |
| MolCRAFTModel Category=De novo 3D-generation2026.05 | 4.44 | -7.679 | — | 0.503 | 0.684 | 24.8 | 63.5 | 22.2 | 1.18 | 327.33 | 13 | — | — | — | — | — | — | — | — | — | — | — | — | |
| LMLFModel Category=De novo 3D-generation2026.05 | 4.43 | -7.776 | — | 0.515 | 0.572 | 8.31 | 23.52 | 25.83 | 4.18 | 327.49 | 23 | — | — | — | — | — | — | — | — | — | — | — | — | |
| ELILLMModel Category=De novo 3D-generation2026.05 | 4.42 | -7.93 | — | 0.528 | 0.579 | 9.81 | 24.02 | 27.93 | 4.22 | 328.09 | 22 | — | — | — | — | — | — | — | — | — | — | — | — | |
| DecompDiffModel Category=De novo 3D-generation2026.05 | 4.31 | -7.949 | — | 0.449 | 0.604 | 19.8 | 64.24 | 28.89 | 2.45 | 424.14 | 18 | — | — | — | — | — | — | — | — | — | — | — | — | |
| Reference2026.05 | 4.27 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | |
| DecompDPOModel Category=De novo 3D-generation2026.05 | 4.2 | -8.427 | — | 0.471 | 0.662 | 30.4 | 55.1 | 15.8 | 5.01 | 435.33 | 9 | — | — | — | — | — | — | — | — | — | — | — | — | |
| ALIDiffMethod Category=Comp. w/ diff.+opt.2026.05 | — | — | — | — | — | — | — | — | — | — | — | -8.09 | -8.17 | -7.07 | -7.95 | 73.4 | 81.4 | 0.5 | 0.57 | 0.73 | — | — | — | |
| ALIDiff2026.05 | — | — | — | — | — | 46.6 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | 21.3 | 14.1 | 92.4 | |
| ARMethod Category=Comp. w/ Non-diff.2026.05 | — | — | — | — | — | — | — | — | — | — | — | -6.18 | -5.88 | -5.75 | -5.64 | 37.9 | 31 | 0.51 | 0.63 | 0.7 | — | — | — | |
| AR2026.05 | — | — | — | — | — | 20.3 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | 12.4 | 7.7 | 93 | |
| DecompDiffAggregate size=100 pockets, Scoring method=AutoDock Vina2025.12 | — | -8.39 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | |
| DecompDiffMethod Category=Comp. w/ diff.2026.05 | — | — | — | — | — | — | — | — | — | — | — | -7.04 | -7.09 | -5.67 | -6.04 | 64.4 | 71 | 0.45 | 0.61 | 0.68 | — | — | — | |
| DecompOptMethod Category=Comp. w/ diff.+opt.2026.05 | — | — | — | — | — | — | — | — | — | — | — | -7.35 | -7.72 | -5.87 | -6.81 | 73.5 | 93.3 | 0.48 | 0.65 | 0.6 | — | — | — | |
| FTDiffOptimization Setting=Single-objective2026.05 | — | -8.11 | -8.25 | — | — | — | — | — | — | — | — | -9.41 | -9.28 | -10.22 | -10.09 | 80.7 | 89 | 0.49 | 0.53 | 0.75 | — | — | — | |
| FTDiffMethod Category=Comp. w/ Non-diff.2026.05 | — | — | — | — | — | — | — | — | — | — | — | -8.48 | -8.53 | -7.18 | -7.73 | 78.6 | 88.9 | 0.56 | 0.61 | 0.72 | — | — | — | |
| FTDiffMethod Category=Comp. w/ diff.2026.05 | — | — | — | — | — | — | — | — | — | — | — | -8.48 | -8.53 | -7.18 | -7.73 | 78.6 | 88.9 | 0.56 | 0.61 | 0.72 | — | — | — | |
| FTDiffMethod Category=Comp. w/ diff.+opt.2026.05 | — | — | — | — | — | — | — | — | — | — | — | -8.48 | -8.53 | -7.18 | -7.73 | 78.6 | 88.9 | 0.56 | 0.61 | 0.72 | — | — | — | |
| FTDiff2026.05 | — | — | — | — | — | 47.4 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | 30.4 | 22.3 | 95.8 | |
| GraphBPMethod Category=Comp. w/ Non-diff.2026.05 | — | — | — | — | — | — | — | — | — | — | — | — | — | -4.8 | -4.7 | 17.2 | 6.7 | 0.43 | 0.49 | 0.79 | — | — | — | |
| IPDiffMethod Category=Comp. w/ diff.2026.05 | — | — | — | — | — | — | — | — | — | — | — | -7.45 | -7.48 | -6.42 | -7.01 | 69.5 | 75.5 | 0.52 | 0.61 | 0.74 | — | — | — | |
| KGDiffOptimization Setting=Single-objective2026.05 | — | -8.04 | -8.61 | — | — | — | — | — | — | — | — | -8.78 | -8.85 | -9.43 | -9.43 | 79.2 | 87 | 0.51 | 0.54 | 0.75 | — | — | — | |
| LiGANMethod Category=Comp. w/ Non-diff.2026.05 | — | — | — | — | — | — | — | — | — | — | — | — | — | -6.33 | -6.2 | 21.1 | 11.1 | 0.39 | 0.59 | 0.66 | — | — | — | |
| MolCRAFTMethod Category=Comp. w/ Non-diff.2026.05 | — | — | — | — | — | — | — | — | — | — | — | -7.27 | -7.26 | -6.59 | -7.04 | 59.1 | 62.6 | 0.5 | 0.68 | 0.72 | — | — | — | |
| MolCRAFT2026.05 | — | — | — | — | — | 36.2 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | 17.5 | 16.7 | 96.7 | |
| Pocket2MolAggregate size=100 pockets, Scoring method=AutoDock Vina2025.12 | — | -7.15 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | |
| Pocket2MolMethod Category=Comp. w/ Non-diff.2026.05 | — | — | — | — | — | — | — | — | — | — | — | -6.42 | -5.82 | -5.14 | -4.7 | 48.4 | 51 | 0.56 | 0.74 | 0.69 | — | — | — | |
| Pocket2Mol2026.05 | — | — | — | — | — | 16.2 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | 8.9 | 8.4 | 98.3 | |
| ReferenceOptimization Setting=Single-objective2026.05 | — | -6.36 | -6.46 | — | — | — | — | — | — | — | — | -6.71 | -6.49 | -7.45 | -7.26 | — | — | 0.48 | 0.73 | — | — | — | — | |
| Reference2026.05 | — | — | — | — | — | — | — | — | — | — | — | -6.71 | -6.49 | -6.36 | -6.46 | — | — | 0.48 | 0.73 | — | — | — | — | |
| RxnFlowAggregate size=100 pockets, Scoring method=AutoDock Vina2025.12 | — | -8.85 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | |
| TacoGFNAggregate size=100 pockets, Scoring method=AutoDock Vina2025.12 | — | — | -8.82 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | |
| TAGMolMethod Category=Comp. w/ diff.+opt.2026.05 | — | — | — | — | — | — | — | — | — | — | — | -7.95 | -8.07 | -7.02 | -7.77 | 69.8 | 76.4 | 0.55 | 0.56 | 0.69 | — | — | — | |
| TAGMol2026.05 | — | — | — | — | — | 47 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | 27.9 | 17.4 | 92 | |
| TargetDiffAggregate size=100 pockets, Scoring method=AutoDock Vina2025.12 | — | -7.8 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | — | |
| TargetDiffMethod Category=Comp. w/ diff.2026.05 | — | — | — | — | — | — | — | — | — | — | — | -6.64 | -6.83 | -5.47 | -6.3 | 58.1 | 59.1 | 0.48 | 0.58 | 0.72 | — | — | — | |
| TargetDiff2026.05 | — | — | — | — | — | 26.3 | — | — | — | — | — | — | — | — | — | — | — | — | — | — | 12.5 | 8.6 | 90.4 |