Using Flory effect to improve protein unfolding pathway visualization
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Authors
San, Wenyin
Issue Date
2017-12
Type
Electronic thesis
Thesis
Thesis
Language
ENG
Keywords
Computer science
Alternative Title
Abstract
The 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.
Description
December 2017
School of Science
School of Science
Full Citation
Publisher
Rensselaer Polytechnic Institute, Troy, NY