PDBBind
Benchmarks
TaskDatasetSOTA resultTrendResults
PDBbind Sequence Identity (30%) 2017
1.295RMSE
82
PDBbind Sequence Identity (60%) 2017
1.175RMSE
50
PDBbind Core Set v2016
1.099RMSE
47
PDBbind core set 2013
1.193RMSE
41
PDBbind 2019 (holdout set)
1.321RMSE
38
PDBbind v2020 (unseen protein receptors)
40.8Ligand RMSD % < 2Å Success Rate
24
PDBbind 2016 (core set)
1.107RMSE
22
PDBbind core set (random split)
1.202RMSE
21
PDBBind Apo ESMFold proteins generated (test)
24.9Top-1 RMSD < 2Å Acc
21
PDBbind
1.263RMSE
20
PDBBind core set 2016 (test)
0.83R
17
PDBBind (unseen receptors)
20.8Top-1 RMSD < 2Å (%)
17
PDBbind core set (test)
1.316RMSE
16
PDBbind (test)
1.309RMSE
15
PDBbind v2020 (test)
1.2Ligand RMSD (25%)
14
PDBBind (unseen receptors)
1.6Ligand RMSD (25p)
14
PDBbind 2020
0Failure Rate
13
PDBBind core set v2016
-7.76Vina Score
12
PDBbind v2020 (Time Split (363))
47.9RMSD < 2.0Å Success
12
PDBbind v2020 (test complexes recorded after 2019)
1.5Ligand RMSD (25th Pctl)
12
PDBBind time 2020
1.26RMSE
11
PDBbind LBA (test)
1.321RMSE
11
PDBbind (Scaffold)
1.248RMSE
11
PDBbind (Random split)
1.214RMSE
11
PDBBind Holo crystal proteins (test)
0.382Top-1 RMSD < 2Å (%)
11