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Parameter Choice Matters: Validating Probe Parameters for Use in Mixed-Solvent Simulations
2014
Journal of Chemical Information and Modeling
Probe mapping is a common approach for identifying potential binding sites in structure-based drug design; however, it typically relies on energy minimizations of probes in the gas phase and a static protein structure. The mixed-solvent molecular dynamics (MixMD) approach was recently developed to account for full protein flexibility and solvation effects in hot-spot mapping. Our first study used only acetonitrile as a probe, and here, we have augmented the set of functional group probes
doi:10.1021/ci400741u
pmid:25058662
pmcid:PMC4144759
fatcat:ija2xcsnmbhvvktueprsetqxz4