@article{e902d0279b47478b9a0bf69721449ae9,
title = "End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design",
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.",
author = "Ercheng Wang and Huiyong Sun and Junmei Wang and Zhe Wang and Hui Liu and Zhang, {John Z.H.} and Tingjun Hou",
note = "Funding Information: This work was financially supported by the National Key R&D Program of China (2016YFA0501700 and 2016YFB0201700), the National Natural Science Foundation of China (21575128, 81773632, 21433004, and 91753103), the Innovation Program of Shanghai Municipal Education Commission (201701070005E00020), and the National Institutes of Health (R01-GM079383 and R21-GM097617). Funding Information: John Z. H. Zhang received his Ph.D. in chemical physics in 1987. His current research focuses on computational studies of biomolecular systems, including protein–ligand binding, protein–protein interaction, protein design, etc. He is currently the director of the NYU–ECNU Center for Computational Chemistry at NYU Shanghai and a professor of chemistry at NYU Shanghai and ECNU. He has won many awards and fellowships, including the Camille and Henry Dreyfus New Faculty Award (1990), the National Science Foundation Presidential Faculty Fellowship (1994), the Alfred P. Sloan Foundation Research Fellowship (1995), and the Camille Dreyfus Teacher-Scholar Award (1995). He has over 350 publications in peer-reviewed journals with an h-index of 55. Funding Information: This work was financially supported by the National Key R&D Program of China (2016YFA0501700 and 2016YFB0201700), the National Natural Science Foundation of China (21575128, 81773632, 21433004, and 91753103), the Innovation Program of Shanghai Municipal Education Commission (201701070005E00020), and the National Institutes of Health (R01-GM079383 and R21-GM097617). Publisher Copyright: {\textcopyright} 2019 American Chemical Society.",
year = "2019",
month = aug,
day = "28",
doi = "10.1021/acs.chemrev.9b00055",
language = "English (US)",
volume = "119",
pages = "9478--9508",
journal = "Chemical Reviews",
issn = "0009-2665",
publisher = "American Chemical Society",
number = "16",
}