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dc.contributor.authorLee, En-Shiun Annie
dc.date.accessioned2008-09-26 18:23:09 (GMT)
dc.date.available2008-09-26 18:23:09 (GMT)
dc.date.issued2008-09-26T18:23:09Z
dc.date.submitted2008
dc.identifier.urihttp://hdl.handle.net/10012/4060
dc.description.abstractThreading is a protein structure prediction method that uses a library of template protein structures in the following steps: first the target sequence is matched to the template library and the best template structure is selected, secondly the predicted target structure of the target sequence is modeled by this selected template structure. The deceleration of new folds which are added to the protein data bank promises completion of the template structure library. This thesis uses a new set of template-specific weights to improve the energy function for sequence-to-structure alignment in the template selection step of the threading process. The weights are estimated using least squares methods with the quality of the modelling step in the threading process as the label. These new weights show an average 12.74% improvement in estimating the label. Further family analysis show a correlation between the performance of the new weights to the number of seeds in pFam.en
dc.language.isoenen
dc.publisherUniversity of Waterlooen
dc.subjectBioinformaticsen
dc.subjectProtein Structure Predictionen
dc.subjectComparative Modellingen
dc.subjectEnergy Functionen
dc.subjectSequence-to-Structure Alignmenten
dc.subjectTemplate Selectionen
dc.subjectThreadingen
dc.subjectMachine Learningen
dc.subjectWeighted Linear Least Squaresen
dc.titleTraining of Template-Specific Weighted Energy Function for Sequence-to-Structure Alignmenten
dc.typeMaster Thesisen
dc.comment.hiddenSuggested formatting changes I have made: 1. Title page - degree is incorrect. It must read: Master of Mathematics. 2. Table of contents - add List of Figures and List of Tables titles to the Table of contents list (above the Chapter 1 Introduction title). 3. Table of contents - add an Appendix title above the 'A Formulation...' appendix to the Table of contents list. 4. Remove the words 'List of' from the References title. Add a References title to the Table of contents list. (Do not include it as a chapter).en
dc.pendingfalseen
dc.subject.programComputer Scienceen
uws-etd.degree.departmentSchool of Computer Scienceen
uws-etd.degreeMaster of Mathematicsen
uws.typeOfResourceTexten
uws.peerReviewStatusUnrevieweden
uws.scholarLevelGraduateen


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