Recent Developments and Applications of the MMPBSA Method

Changhao Wang; D'Artagnan Greene; Li Xiao; Ruxi Qi; Ray Luo

doi:10.3389/fmolb.2017.00087

Recent Developments and Applications of the MMPBSA Method

Front Mol Biosci. 2018 Jan 10:4:87. doi: 10.3389/fmolb.2017.00087. eCollection 2017.

Authors

Changhao Wang^{1

2

3}, D'Artagnan Greene², Li Xiao^{2

4}, Ruxi Qi², Ray Luo^{1

2

4

5}

Affiliations

¹ Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States.
² Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States.
³ Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States.
⁴ Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States.
⁵ Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States.

Abstract

The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.

Keywords: MMPBSA; binding affinity; continuum solvation model; free energy simulation; molecular recognition.

Publication types

Review

Abstract

Publication types

Grants and funding