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Table 2 Summary of docking results on the targets with binding site error < 8 Å

From: EDock: blind protein–ligand docking by replica-exchange monte carlo simulation

DatasetsMethodsRMSD (Å)Center distance (Å)Ave RMSD < 2.0 Å
AveMedAveMed
DUDE (76)EDock1.450.330.880.2364
DOCK62.030.541.170.3757
Vina3.922.732.051.1336
Vinablind5.151.153.500.9240
COACH (315)EDock2.170.431.210.33221
DOCK62.840.901.560.51190
Vina3.922.961.921.10139
Vinablind7.376.075.652.83101
  1. Since 4 (and 8) test targets failed in Vina (and DOCK6), only 391 targets (76 from DUDE and 315 from COACH), on which all programs have a result, are shown. “Ave” and “Med” represent the average and median values respectively. “EDock”, “DOCK6” and “Vina” represent the results starting with the same binding sites predicted by COACH, while “Vinablind” refers to the blind docking result of AutoDock Vina with searching the whole receptor space. The best performance is highlighted in italic font in each category