Journal
CHEMICAL REVIEWS
Volume 119, Issue 16, Pages 9478-9508Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.chemrev.9b00055
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Funding
- National Key R&D Program of China [2016YFA0501700, 2016YFB0201700]
- National Natural Science Foundation of China [21575128, 81773632, 21433004, 91753103]
- Innovation Program of Shanghai Municipal Education Commission [201701070005E00020]
- National Institutes of Health [R01-GM079383, R21-GM097617]
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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.
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