End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

Ercheng Wang, Huiyong Sun, Junmei Wang, Zhe Wang, Hui Liu, John Z.H. Zhang, Tingjun Hou

Research output: Contribution to journalReview articlepeer-review

Abstract

Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) and molecular mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods for binding free energy prediction since they are more accurate than most scoring functions of molecular docking and less computationally demanding than alchemical free energy methods. MM/PBSA and MM/GBSA have been widely used in biomolecular studies such as protein folding, protein-ligand binding, protein-protein interaction, etc. In this review, methods to adjust the polar solvation energy and to improve the performance of MM/PBSA and MM/GBSA calculations are reviewed and discussed. The latest applications of MM/GBSA and MM/PBSA in drug design are also presented. This review intends to provide readers with guidance for practically applying MM/PBSA and MM/GBSA in drug design and related research fields.

Original languageEnglish (US)
Pages (from-to)9478-9508
Number of pages31
JournalChemical reviews
Volume119
Issue number16
DOIs
StatePublished - Aug 28 2019

ASJC Scopus subject areas

  • Chemistry(all)

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