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Table 1 Summary of docking results on holo-protein structures with known ligand binding sites

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

DatasetsMethodsLigand RMSD (Å)Center distance (Å)Ave RMSD < 1.0 Å
AveMedAveMed
DUDE (101)Initial4.173.721.971.557
EDock1.280.360.740.2681
Vina1.380.520.670.3580
DOCK61.410.530.900.3281
COACH (429)Initial3.903.131.611.2635
EDock1.910.480.990.35286
Vina2.720.781.360.56228
DOCK62.721.461.140.77171
  1. Since 4 (and 1) of 535 test targets failed in Vina (and DOCK6), only 530 targets (101 from DUDE and 429 from COACH), on which all programs have a result, are shown. “Initial” refers to initial poses from graph matching with the highest XSCORE; “Ave” and “Med” represents the average and median values, respectively. The best performance is highlighted in italic font in each category