Bingjie Hu

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Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the(More)
Virtual screening using pharmacophore models is an efficient method to identify potential lead compounds for target proteins. Pharmacophore models based on protein structures are advantageous because a priori knowledge of active ligands is not required and the models are not biased by the chemical space of previously identified actives. However, in order to(More)
Protein-based pharmacophore models derived from protein binding site atoms without the inclusion of any ligand information have become more popular in virtual screening studies. However, the accuracy of protein-based pharmacophore models for reproducing the critical protein-ligand interactions has never been explicitly assessed. In this study, we used known(More)
Water contributes significantly to the binding of small molecules to proteins in biochemical systems. Molecular dynamics (MD) simulation based programs such as WaterMap and WATsite have been used to probe the locations and thermodynamic properties of hydration sites at the surface or in the binding site of proteins generating important information for(More)
Water molecules that mediate protein-ligand interactions or are released from the binding site on ligand binding can contribute both enthalpically and entropically to the free energy of ligand binding. To elucidate the thermodynamic profile of individual water molecules and their potential contribution to ligand binding, a hydration site analysis program(More)
  • Bingjie Hu, Directed, Peter Murrell, Harry Kelejian, Erik Lichtenberg, Raymond Guiteras +1 other
  • 2011
This thesis consists of three chapters on the choice of institutional governance. The first chapter provides empirical evidence on the effect of local norms on the contractual choice, using a comprehensive dataset on US agricultural leasing contracts. We focus on the choice between cash-rent and share-rent contracts and examine whether the prevalence of(More)
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