Drug efficiency indices for improvement of molecular docking scoring functions

Alfonso T. García-Sosa, Csaba Hetényi, U. K.O. Maran

Research output: Contribution to journalArticle

34 Citations (Scopus)


A dataset of protein-drug complexes with experimental binding energy and crystal structure were analyzed and the performance of different docking engines and scoring functions (as well as components of these) for predicting the free energy of binding and several ligand efficiency indices were compared. The aim was not to evaluate the best docking method, but to determine the effect of different efficiency indices on the experimental and predicted free energy. Some ligand efficiency indices, such as ΔG/W (Wiener index), ΔG/NoC (number of carbons), and ΔG/P (partition coefficient), improve the correlation between experimental and calculated, values. This effect was shown to be valid across the different scoring functions and docking programs. It also removes the common bias of scoring functions in favor of larger ligands. For all scoring functions, the efficiency indices effectively normalize the free energy derived indices, to give values closer to experiment. Compound collection filtering can be done prior or after docking, using pharmacokinetic as well as pharmacodynamic profiles. Achieving these better correlations with experiment can improve the ability of docking scoring functions to predict active molecules in virtual screening.

Original languageEnglish
Pages (from-to)174-184
Number of pages11
JournalJournal of Computational Chemistry
Issue number1
Publication statusPublished - Jan 15 2010


  • Docking
  • Drug design
  • Free energy of binding
  • Scoring function
  • Virtual screening

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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