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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.