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dc.contributor.advisorRen, Pengyu
dc.creatorZhang, Jiajingen 2011en
dc.description.abstractA central goal of computational biophysics and biochemistry is to understand the behavior, interactions, and reactions of molecules, and to interpret and facilitate experimental design. The objective of this thesis research is to use the molecular modeling and simulation techniques to advance our understanding of principles in molecular structure properties, recognition and interaction at the atomic level. First, a physical molecular mechanics model is built to study the conformational properties of depsipeptide, which shows potential for engineered protein mimetics with controllable structure and function. We explore the possible kinase-substrate binding modes and the likelihood of an [alpha]-helix docking interaction within a kinase active site. Finally, efficient physical models based on a polarizable potential function are developed to describe the structural properties and calculate protein-ligand binding affinities accurately for both trypsin and matrix metalloproteinase.en
dc.subjectMolecular modelingen
dc.subjectMolecular dynamics simulationen
dc.subjectProtein-ligand binding free energy calculationen
dc.titleInsight into biomolecular structure, interaction and energetics from modeling and simulationen
dc.description.departmentBiomedical Engineeringen

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