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dc.rights.licenseRestricted to current Rensselaer faculty, staff and students. Access inquiries may be directed to the Rensselaer Libraries.
dc.contributorBystroff, Christopher, 1960-
dc.contributorZaki, Mohammed J., 1971-
dc.contributorKrishnamoorthy, M. S.
dc.contributor.authorSan, Wenyin
dc.date.accessioned2021-11-03T08:55:42Z
dc.date.available2021-11-03T08:55:42Z
dc.date.created2018-02-21T13:07:43Z
dc.date.issued2017-12
dc.identifier.urihttps://hdl.handle.net/20.500.13015/2109
dc.descriptionDecember 2017
dc.descriptionSchool of Science
dc.description.abstractThe problem of protein folding is listed as an important issue in 21st century biophysics. It is a fundamental problem in the central dogma of molecular biology. Predicting the tertiary structure of protein molecules from primary sequences and further predicting their functions are challenging tasks. Knowledge of protein folding pathways can give us insight into how proteins function, how they cause diseases, and even how they can be improved. In the Bystroff lab, a program GeoFold is developed for predicting protein unfolding pathways, the reverse of folding pathways and kinetics. In this thesis, we develop an algorithm to find effecitve Loop Length in GeoFold. To begin with, we show why Flory effect is an entropic component when energy of GeoFold hierarchical partitions are measured. Then we will perform an algorithm of Shortest Path based on Dijkstra for calculating effective loop length in Fortran. To demonstrate the result of Flory effect in GeoFold, it will be used in the analysis of a test case including a mini protein of Trp-Cage.
dc.language.isoENG
dc.publisherRensselaer Polytechnic Institute, Troy, NY
dc.relation.ispartofRensselaer Theses and Dissertations Online Collection
dc.subjectComputer science
dc.titleUsing Flory effect to improve protein unfolding pathway visualization
dc.typeElectronic thesis
dc.typeThesis
dc.digitool.pid178741
dc.digitool.pid178742
dc.digitool.pid178743
dc.rights.holderThis electronic version is a licensed copy owned by Rensselaer Polytechnic Institute, Troy, NY. Copyright of original work retained by author.
dc.description.degreeMS
dc.relation.departmentDept. of Computer Science


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