Date of Award
Spring 5-2015
Degree Type
Thesis
Degree Name
M.S.
Degree Program
Computer Science
Department
Computer Science
Major Professor
Hoque, Md Tamjidul
Abstract
Energy functions are found to be a key of protein structure prediction. In this work, we propose a novel 3-dimensional energy function based on hydrophobic-hydrophilic properties of amino acid where we consider at least three different possible interaction of amino acid in a 3-dimensional sphere categorized as hydrophilic versus hydrophilic, hydrophobic versus hydrophobic and hydrophobic versus hydrophilic. Each of these interactions are governed by a 3-dimensional parameter alpha used to model the interaction and 3-dimensional parameter beta used to model weight of contribution. We use Genetic Algorithm (GA) to optimize the value of alpha, beta and Z-score. We obtain three energy scores libraries from a database of 4332 protein structures obtained from Protein Data Bank (PDB) server. Proposed energy function is found to outperform nearest competitor by 40.9% for the most challenging Rosetta decoy as well as better in terms of the Z-score based on Moulder and Rosetta decoy sets.
Recommended Citation
Mishra, Avdesh, "Three-Dimensional Ideal Gas Reference State based Energy Function" (2015). University of New Orleans Theses and Dissertations. 1986.
https://scholarworks.uno.edu/td/1986
Included in
Biochemical and Biomolecular Engineering Commons, Biochemistry Commons, Bioinformatics Commons, Biophysics Commons, Computational Engineering Commons, Molecular Biology Commons, Structural Biology Commons
Rights
The University of New Orleans and its agents retain the non-exclusive license to archive and make accessible this dissertation or thesis in whole or in part in all forms of media, now or hereafter known. The author retains all other ownership rights to the copyright of the thesis or dissertation.