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Table 1 Comparison of PharmDock with docking programs evaluated by Plewczynski et al .

From: PharmDock: a pharmacophore-based docking program

 

Native conformation as docking input1

Omega conformations as docking input2

 

avg RMSDtop(Å)

%entries ≤ 2 Å

avg RMSDtop(Å)

%entries ≤ 2 Å

Surflex

3.2

52%

3.1

51%

GOLD

2.8

55%

2.4

63%

eHiTs

N/A

N/A

2.6

58%

Glide SP

3.3

52%

3.7

43%

AutoDock

2.3

56%

4.0

41%

LigandFit

3.2

48%

4.4

33%

FlexX

4.2

41%

4.3

37%

PharmDock

2.9

56%

3.9

37%

  1. Avg RMSDtop: RMSDtop averaged over all the tested complexes. %entries ≤ 2 Å: the fraction of complexes with RMSDtop ≤ 2 Å. The results for the seven docking programs in comparison were extracted from Plewczynski et al.’s study [31]. 1In Plewczynski et al.’s study, only the native ligand conformation is provided. In PharmDock simulations, the native ligand conformation is seeded within the Omega-generated low energy conformations, because PharmDock does not generate ligand conformations on-the-fly during pose sampling. Conformations are further modified during pose optimization. All other docking programs take the input ligand conformation and re-generate multiple ligand conformations during the search process. 2Plewczynski et al. generated ten low-energy conformers per ligand using Omega for their study.