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- W2895846624 endingPage "3269" @default.
- W2895846624 startingPage "3269" @default.
- W2895846624 abstract "Simulations of molecular dynamics (MD) are playing an increasingly important role in structure-based drug discovery (SBDD). Here we review the use of MD for proteins in aqueous solvation, organic/aqueous mixed solvents (MDmix) and with small ligands, to the classic SBDD problems: Binding mode and binding free energy predictions. The simulation of proteins in their condensed state reveals solvent structures and preferential interaction sites (hot spots) on the protein surface. The information provided by water and its cosolvents can be used very effectively to understand protein ligand recognition and to improve the predictive capability of well-established methods such as molecular docking. The application of MD simulations to the study of the association of proteins with drug-like compounds is currently only possible for specific cases, as it remains computationally very expensive and labor intensive. MDmix simulations on the other hand, can be used systematically to address some of the common tasks in SBDD. With the advent of new tools and faster computers we expect to see an increase in the application of mixed solvent MD simulations to a plethora of protein targets to identify new drug candidates." @default.
- W2895846624 created "2018-10-26" @default.
- W2895846624 creator A5023804925 @default.
- W2895846624 creator A5035789659 @default.
- W2895846624 creator A5037789245 @default.
- W2895846624 creator A5048854608 @default.
- W2895846624 creator A5081101274 @default.
- W2895846624 creator A5089022257 @default.
- W2895846624 date "2018-12-11" @default.
- W2895846624 modified "2023-10-16" @default.
- W2895846624 title "Solvents to Fragments to Drugs: MD Applications in Drug Design" @default.
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