A comprehensive docking and MM/GBSA rescoring study of ligand recognition upon binding antithrombin

Xiaohua Zhang, Horacio Perez-Sanchez, Felice C Lightstone

Research output: Contribution to journalArticlepeer-review

55 Scopus citations


Background: A high-throughput virtual screening pipeline has been extended from single energetically minimized structure Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) rescoring to ensemble-average MM/GBSA rescoring. The correlation coefficient (R2) of calculated and experimental binding free energies for a series of antithrombin ligands has been improved from 0.36 to 0.69 when switching from the single-structure MM/GBSA rescoring to ensemble-average one. The electrostatic interactions in both solute and solvent are identified to play an important role in determining the binding free energy after the decomposition of the calculated binding free energy. The increasing negative charge of the compounds provides a more favorable electrostatic energy change but creates a higher penalty for the solvation free energy. Such a penalty is compensated by the electrostatic energy change, which results in a better binding affinity. A highly hydrophobic ligand is determined by the docking program to be a non-specific binder. Results: Our results have demonstrated that it is very important to keep a few top poses for rescoring, if the binding is non-specific or the binding mode is not well determined by the docking calculation.

Original languageEnglish (US)
Pages (from-to)1631-1639
Number of pages9
JournalCurrent Topics in Medicinal Chemistry
Issue number14
StatePublished - May 1 2017
Externally publishedYes


  • Antithrombin
  • Binding Affinity
  • Docking
  • Molecular Dynamics
  • Rescoring
  • VinaLC

ASJC Scopus subject areas

  • Medicine(all)


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