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Sampling biomolecular conformations with spatial and energetic constraints

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dc.contributor.advisor Kavraki, Lydia E.
dc.creator Shehu, Amarda
dc.date.accessioned 2009-06-04T08:39:36Z
dc.date.available 2009-06-04T08:39:36Z
dc.date.issued 2005
dc.identifier.uri http://hdl.handle.net/1911/17825
dc.description.abstract This work extends cyclic coordinate descent to efficiently satisfy multiple spatial constraints, respect the secondary structure of proteins., and work with reduced backbone protein models. Reduced models allow us to treat large systems that are intractable under all-atom models. In addition, this thesis combines the satisfaction of multiple spatial constraints with conformational sampling and energy minimization techniques to generate spatially constrained biomolecular structures that are energetically stable under physiological conditions. The experiments in this thesis demonstrate the relevance and robustness of our method on three areas of applications: loop closure; backbone reconstruction, and physical trajectory recovery. Addressing the problem of loop closure, we obtain ensembles of spatially constrained conformations whose energy landscape is in agreement with laboratory experimental results on the energetic stability of the proteins at hand. Our experiments on backbone reconstruction agree with results from statistical approaches to this problem, but in addition guarantee the energetic feasibility of the completed models. (Abstract shortened by UMI.)
dc.format.extent 90 p.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.subject Biology, Molecular
Computer Science
Biology
Computer Science
dc.title Sampling biomolecular conformations with spatial and energetic constraints
dc.type.genre Thesis
dc.type.material Text
thesis.degree.department Biology
thesis.degree.discipline Natural Sciences
thesis.degree.grantor Rice University
thesis.degree.level Masters
thesis.degree.name Master of Science
dc.identifier.citation Shehu, Amarda. (2005) "Sampling biomolecular conformations with spatial and energetic constraints." Masters Thesis, Rice University. http://hdl.handle.net/1911/17825.

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