Using free energy of binding calculations to improve the accuracy of virtual screening predictions

Robert D. Malmstrom, Stanley J. Watowich

Research output: Contribution to journalArticlepeer-review

24 Scopus citations


Virtual screening of small molecule databases against macromolecular targets was used to identify binding ligands and predict their lowest energy bound conformation (i.e., pose). AutoDock4-generated poses were rescored using mean-field pathway decoupling free energy of binding calculations and evaluated if these calculations improved virtual screening discrimination between bound and nonbound ligands. Two small molecule databases were used to evaluate the effectiveness of the rescoring algorithm in correctly identifying binders of L99A T4 lysozyme. Self-dock calculations of a database containing compounds with known binding free energies and cocrystal structures largely reproduced experimental measurements, although the mean difference between calculated and experimental binding free energies increased as the predicted bound poses diverged from the experimental poses. In addition, free energy rescoring was more accurate than AutoDock4 scores in discriminating between known binders and nonbinders, suggesting free energy rescoring could be a useful approach to reduce false positive predictions in virtual screening experiments.

Original languageEnglish (US)
Pages (from-to)1648-1655
Number of pages8
JournalJournal of Chemical Information and Modeling
Issue number7
StatePublished - Jul 25 2011

ASJC Scopus subject areas

  • General Chemistry
  • General Chemical Engineering
  • Computer Science Applications
  • Library and Information Sciences


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