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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

Datasets

Methods

Ligand RMSD (Å)

Center distance (Å)

Ave RMSD < 1.0 Å

Ave

Med

Ave

Med

DUDE (101)

Initial

4.17

3.72

1.97

1.55

7

EDock

1.28

0.36

0.74

0.26

81

Vina

1.38

0.52

0.67

0.35

80

DOCK6

1.41

0.53

0.90

0.32

81

COACH (429)

Initial

3.90

3.13

1.61

1.26

35

EDock

1.91

0.48

0.99

0.35

286

Vina

2.72

0.78

1.36

0.56

228

DOCK6

2.72

1.46

1.14

0.77

171

  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