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Recent Developments and Applications of the MMPBSA Method

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Specialty Biology
Date 2018 Jan 26
PMID 29367919
Citations 163
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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.

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References
1.
Wang C, Nguyen P, Pham K, Huynh D, Le T, Wang H . Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. J Comput Chem. 2016; 37(27):2436-46. PMC: 5018451. DOI: 10.1002/jcc.24467. View

2.
Guan S, Han W, Zhang H, Wang S, Shan Y . Insight into the interactive residues between two domains of human somatic Angiotensin-converting enzyme and Angiotensin II by MM-PBSA calculation and steered molecular dynamics simulation. J Biomol Struct Dyn. 2015; 34(1):15-28. DOI: 10.1080/07391102.2015.1007167. View

3.
Gu Y, Wang W, Zhu X, Dong K . Molecular dynamic simulations reveal the mechanism of binding between xanthine inhibitors and DPP-4. J Mol Model. 2014; 20(2):2075. DOI: 10.1007/s00894-014-2075-1. View

4.
Zhan D, Yu L, Jin H, Guan S, Han W . Molecular modeling and MM-PBSA free energy analysis of endo-1,4-β-xylanase from Ruminococcus albus 8. Int J Mol Sci. 2014; 15(10):17284-303. PMC: 4227162. DOI: 10.3390/ijms151017284. View

5.
Bhavaraju M, Hansmann U . Effect of single point mutations in a form of systemic amyloidosis. Protein Sci. 2015; 24(9):1451-62. PMC: 4570539. DOI: 10.1002/pro.2730. View