User:Meeshko/sandbox
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| This is a user sandbox of Meeshko. You can use it for testing or practicing edits. This is not the sandbox where you should draft your assigned article for a dashboard.wikiedu.org course. To find the right sandbox for your assignment, visit your Dashboard course page and follow the Sandbox Draft link for your assigned article in the My Articles section. |
Research Interests
OPLS Force Fields Optimized Potentials for Liquid Simulations (OPLS) is a set of force fields developed by Jorgensen since the 1980s. [1] OPLS was then parameterized according to experimental properties of liquids. These family of OPLS force fields are used in simulations that involve biological systems. [2] There are united atom (OPLS-UA) and all atom (OPLS-AA) force fields. OPLS-UA is a "mixed" force field, where aliphatic groups are contracted to pseudo-carbon (united) atoms and everything else (including aromatic CH groups) is all atom. This simplified parametrization saves simulation time considerably. OPLS-AA accounts for every atom and is well suited for describing intermolecular interactions that can successfully be used for conformational analysis of complex organic molecules [3] OPLS simulations in aqueous solution were developed to work with the TIP4P or TIP3P water model, which are intended to reproduce the experimental bulk water properties with limited computational effort. [4] [5]
Impact on Field of Science and Scientific Community
Jorgensen was the first to demonstrate the power of free energy perturbation calculations for chemical reactions in solutions. [6] Micromolar leads rapidly advanced to prove their utility in the design of potent enzyme inhibitors for multiple targets including HIV reverse transcriptase, FGFR1 kinase, and macrophage migration inhibitory factor (MIF). He showed how optimization combined with computation power could be used to design new and potent anti-HIV-1 agents by employing free energy perturbation calculations. Jorgensen's group also developed and improved a family of OPLS force fields that predicts protein-ligand binding measured over a wide range of targets and ligands with high level of accuracy. [7]
References
[edit]- ^ Jorgensen, W. L. J. Phys. Chem. B, 2015, 119, 624–632.
- ^ Mackerell, A. D., Jr., J. Chem. Theory Comput. 2004, 25, 1584-1604.
- ^ Kaminski, G.; Jorgensen, W. L., J Phys Chem. 1996, 100, 18010.
- ^ Cole, D. J.; Vilseck, J. Z.; Tirado-Rives, J.; Payne, M. C.; Jorgensen, W. L., J. Chem. Theory Comput. 2016, 12, 2312-2323.
- ^ Jorgensen, W. L.; Chandrasekhar, J.; Madura, D.; Impey R. W.; Klein, M. L., J. Chem. Phys. 1983, 79, 926-935.
- ^ Jorgensen, W. L.; Thomas, L. L., J. Comp. Chem. 2008, 9, 869-876.
- ^ Harder, E.; Damm, W.; Maple, J.; Wu, C.; Reboul, M.; Xiang, J. Y.; Wang, L.; Lupyan, D.; Dahlgren, M. K.; Knight, J. L.; Kaus, J. W.; Cerutti, D. S.; Krilov, G.; Jorgensen, W. L.; Abel, R.; Friesner, R. A., J. Chem. Theory Comput. 2015, 12, 281-296.
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