Recent Developments and Applications of the MMPBSA Method

被引：426

作者：

Wang, Changhao ^{[1
,2
,3
]}

Greene, D'Artagnan ^{[2
]}

Xiao, Li ^{[2
,4
]}

Qi, Ruxi ^{[2
]}

Luo, Ray ^{[1
,2
,4
,5
]}

机构：

[1] Univ Calif Irvine, Chem & Mat Phys Grad Program, Irvine, CA 92697 USA

[2] Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92717 USA

[3] Univ Calif Irvine, Dept Phys & Astron, Irvine, CA USA

[4] Univ Calif Irvine, Dept Biomed Engn, Irvine, CA 92697 USA

[5] Univ Calif Irvine, Dept Chem Engn & Mat Sci, Irvine, CA 92697 USA

来源：

FRONTIERS IN MOLECULAR BIOSCIENCES | 2018年 / 4卷

关键词：

molecular recognition; binding affinity; free energy simulation; MMPBSA; continuum solvation model; MOLECULAR-DYNAMICS SIMULATION; BINDING FREE-ENERGY; SOLVATION FREE-ENERGIES; PORPHYRIN-ANTHRAQUINONE HYBRIDS; POISSON-BOLTZMANN METHODS; PROTEIN-FOLDING SIMULATIONS; SIMPLE COMPUTATIONAL MODEL; STRUCTURE-BASED PREDICTION; HYDRATION FREE-ENERGY; HUMAN SERUM-ALBUMIN;

D O I：

10.3389/fmolb.2017.00087

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页数：18

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