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Table 2 Comparison of PharmDock with docking programs evaluated by Li et al .

From: PharmDock: a pharmacophore-based docking program

  Native conformation as docking input1 Low energy conformations as docking input2
Glide XP 65% 48%
GOLD/GoldScore 58% 45%
GOLD/ChemScore 58% 43%
LigandFit 54% 36%
Surflex 51% 41%
PharmDock 56% 37%
  1. Fraction of protein-ligand complexes with RMSDtop ≤ 2 Å for PharmDock in comparison with the four docking programs evaluated by Li et al. [29]. 1Similar as in Table 1, the result using PharmDock is shown for omega-generated conformations seeded with native conformation as input, whereas the results extracted from Li et al.’s study only take the native conformation as docking input. 2Li et al. used “CONFORT” in SYBYL to generate one low energy conformation per ligand for the study.