期刊
JOURNAL OF MEDICINAL CHEMISTRY
卷 57, 期 20, 页码 8530-8539出版社
AMER CHEMICAL SOC
DOI: 10.1021/jm5010418
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资金
- Spanish Ministerio de Economia [SAF2009-08811, SAF2012-33481]
- Catalan government [2014 SGR 1189]
- University of Barcelona
- ICREA Funding Source: Custom
Binding sites present well-defined interaction patterns that putative ligands must meet. Knowing them is essential to guide structure-based drug discovery projects. However, complex aspects of molecular recognition-such as protein flexibility or the effect of aqueous solvation-hinder accurate predictions. This is particularly true for polar contacts, which are heavily influenced by the local environment and the behavior of discrete water molecules. Here we present and validate MDmix (Molecular Dynamics simulations with mixed solvents) as a method that provides much more accurate interaction maps than ordinary potentials (e.g., GRID). Additionally, MDmix also affords water displaceability predictions, with advantages over methods that use pure water as solvent (e.g., inhomogeneous fluid solvation theory). With current MD software and hardware solutions, predictions can be obtained in a matter of hours and visualized in a very intuitive manner. Thus, MDmix is an ideal complement in everyday structure-based drug discovery projects.
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