PDBBind
Benchmarks
| Task Name | Dataset Name | SOTA Result | Trend | |
|---|---|---|---|---|
| Protein-Ligand Binding Affinity Prediction | PDBbind Sequence Identity (30%) 2017 | RMSE1.295 | 82 | |
| Protein-Ligand Binding Affinity Prediction | PDBbind Sequence Identity (60%) 2017 | RMSE1.175 | 50 | |
| Drug-target binding affinity prediction | PDBbind Core Set v2016 | RMSE1.099 | 47 | |
| Protein-Ligand Binding Affinity Prediction | PDBbind core set 2013 | RMSE1.193 | 41 | |
| Protein-Ligand Binding Affinity Prediction | PDBbind 2019 (holdout set) | RMSE1.321 | 38 | |
| Flexible blind self-docking | PDBbind v2020 (unseen protein receptors) | Ligand RMSD % < 2Å Success Rate40.8 | 24 | |
| Binding affinity prediction | PDBbind 2016 (core set) | RMSE1.107 | 22 | |
| Protein-ligand binding affinity prediction | PDBbind core set (random split) | RMSE1.202 | 21 | |
| Blind Docking | PDBBind Apo ESMFold proteins generated (test) | Top-1 RMSD < 2Å Acc24.9 | 21 | |
| Protein-Ligand Binding Affinity Prediction | PDBbind | RMSE1.263 | 20 | |
| Binding affinity prediction | PDBBind core set 2016 (test) | R0.83 | 17 | |
| Molecular Docking | PDBBind (unseen receptors) | Top-1 RMSD < 2Å (%)20.8 | 17 | |
| Protein-ligand binding affinity prediction | PDBbind core set (test) | RMSE1.316 | 16 | |
| Protein-Ligand Binding Affinity Prediction | PDBbind (test) | RMSE1.309 | 15 | |
| Blind self-docking | PDBbind v2020 (test) | Ligand RMSD (25%)1.2 | 14 | |
| Flexible blind self-docking | PDBBind (unseen receptors) | Ligand RMSD (25p)1.6 | 14 | |
| Ligand Binding Site Prediction | PDBbind 2020 | Failure Rate0 | 13 | |
| Interaction-Aware Ligand Design for Binding Pockets | PDBBind core set v2016 | Vina Score-7.76 | 12 | |
| Blind docking | PDBbind v2020 (Time Split (363)) | RMSD < 2.0Å Success47.9 | 12 | |
| Flexible blind self-docking | PDBbind v2020 (test complexes recorded after 2019) | Ligand RMSD (25th Pctl)1.5 | 12 | |
| 3D molecule-protein affinity prediction | PDBBind time 2020 | RMSE1.26 | 11 | |
| Ligand Binding Affinity Prediction | PDBbind LBA (test) | RMSE1.321 | 11 | |
| Binding Affinity Prediction | PDBbind (Scaffold) | RMSE1.248 | 11 | |
| Binding Affinity Prediction | PDBbind (Random split) | RMSE1.214 | 11 | |
| Blind Docking | PDBBind Holo crystal proteins (test) | Top-1 RMSD < 2Å (%)0.382 | 11 |
Showing 25 of 35 rows