Recent advances in free energy calculations with a combination of molecular mechanics and continuum models

Junmei M. Wang, Tingjun Hou, Xiaojie Xu

Research output: Contribution to journalReview article

200 Scopus citations

Abstract

Recently, the combination of state-of-the-art molecular mechanical force fields with continuum solvation models enables us to make relatively accurate predictions of both structures and free energies for macromolecules from molecular dynamics trajectories. The first part of this review is focused on the history and basic theory of free energy calculations based on physically effective energy functions. The second part illustrates the applications of free energy calculations on many biological systems, including proteins, DNA, RNA, protein-ligand, protein-protein, protein-nucleic acid complexes, etc. Finally, the prospective and possible strategies to improve the techniques of MM-PBSA and MM-GBSA is discussed.

Original languageEnglish (US)
Pages (from-to)287-306
Number of pages20
JournalCurrent Computer-Aided Drug Design
Volume2
Issue number3
DOIs
StatePublished - Sep 1 2006

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Keywords

  • Binding free energy
  • Continuum solvation model
  • Free energy
  • MM-GBSA
  • MM-PBSA
  • Molecular mechanics

ASJC Scopus subject areas

  • Molecular Medicine
  • Drug Discovery

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