Insight into biomolecular structure, interaction and energetics from modeling and simulation

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dc.contributor.advisorRen, Pengyu
dc.creatorZhang, Jiajingen
dc.date.accessioned2013-07-08T19:40:03Zen
dc.date.accessioned2017-05-11T22:33:10Z
dc.date.available2017-05-11T22:33:10Z
dc.date.issued2011-12en
dc.date.submittedDecember 2011en
dc.date.updated2013-07-08T19:40:03Zen
dc.descriptiontexten
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.description.departmentBiomedical Engineeringen
dc.embargo.lift12/1/2012en
dc.embargo.terms12/1/2012en
dc.format.mimetypeapplication/pdfen
dc.identifier.urihttp://hdl.handle.net/2152/ETD-UT-2011-12-4862en
dc.identifier.urihttp://hdl.handle.net/2152/20672en
dc.language.isoen_USen
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

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University of Texas at Austin