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PDBBind

Benchmarks

Task NameDataset NameSOTA ResultTrend
Flexible blind self-dockingPDBbind v2020 (unseen protein receptors)
Ligand RMSD % < 2Å Success Rate40.8
24
Blind DockingPDBBind Apo ESMFold proteins generated (test)
Top-1 RMSD < 2Å Acc24.9
21
Binding affinity predictionPDBBind core set 2016 (test)
R0.83
17
Molecular DockingPDBBind (unseen receptors)
Top-1 RMSD < 2Å (%)20.8
17
Protein-Ligand Binding Affinity PredictionPDBbind
RMSE1.263
16
Protein-ligand binding affinity predictionPDBbind core set (test)
RMSE1.316
16
Blind self-dockingPDBbind v2020 (test)
Ligand RMSD (25%)1.2
14
Flexible blind self-dockingPDBBind (unseen receptors)
Ligand RMSD (25p)1.6
14
Blind dockingPDBbind v2020 (Time Split (363))
RMSD < 2.0Å Success47.9
12
Flexible blind self-dockingPDBbind v2020 (test complexes recorded after 2019)
Ligand RMSD (25th Pctl)1.5
12
Blind DockingPDBBind Holo crystal proteins (test)
Top-1 RMSD < 2Å (%)0.382
11
Protein-Ligand Binding Affinity PredictionPDBbind Sequence Identity (60%) 2017
RMSE1.365
10
Protein-Ligand Binding Affinity PredictionPDBbind Sequence Identity (30%) 2017
RMSE1.429
10
RegressionPDBbind MoleculeNet (test)
RMSE1.219
9
Molecular DockingPDBBind Full (test)
Top-1 Success Rate (2Å)38.2
8
Protein Pocket DesignPDBBind RNA (test)
AAR44.69
8
Protein-Ligand Binding Affinity PredictionPDBbind 2017 (Scaffold)
RMSE1.516
8
Binding affinity predictionPDBbind 2016 (core set)
RMSE1.316
5
Protein-ligand holo state predictionPDBBind (test)
Ligand RMSD (25th Percentile)4.178
3
Binding Pocket PredictionPDBbind (test)
DCC < 3.0 Å54.8
2
Protein-ligand binding affinity predictionPDBbind 2016
Memory (GB)13.1
2
Regression-based molecular property predictionpdbbind (random split)
RMSE1.391
2
Molecular property predictionpdbbind (scaffold)
RMSE1.397
2
molecule property predictionPDBBind
Metric-
0
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