PharmDock: a pharmacophore-based docking program

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

	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%

Fraction of protein-ligand complexes with RMSD_top ≤ 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.

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