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    • 2013 Dissertations (UMKC)
    • 2013 UMKC Dissertations - Freely Available Online
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    Calculating the structure-based phylogenetic relationship of distantly related homologous proteins utilizing maximum likelihood structural alignment combinatorics and a novel structural molecular clock hypothesis

    Foy, Scott Garrett, 1982-
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    [PDF] CALCULATING THE STRUCTURE-BASED PHYLOGENETIC RELATIONSHIP OF DISTANTLY RELATED HOMOLOGOUS PROTEINS UTILIZING MAXIMUM LIKELIHOOD STRUCTURAL ALIGNMENT COMBINATORICS AND A NOVEL STRUCTURAL MOLECULAR CLOCK HYPOTHESIS (2.754Mb)
    Date
    2013
    Format
    Thesis
    Metadata
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    Abstract
    Dendrograms establish the evolutionary relationships and homology of species, proteins, or genes. Homology modeling, ligand binding, and pharmaceutical testing all depend upon the homology ascertained by dendrograms. Regardless of the specific algorithm, all dendrograms that ascertain protein evolutionary homology are generated utilizing polypeptide sequences. However, because protein structures superiorly conserve homology and contain more biochemical information than their associated protein sequences, I hypothesize that utilizing the structure of a protein instead of its sequence will generate a superior dendrogram. Generating a dendrogram utilizing protein structure requires a unique methodology and novel bioinformatic programs to implement this methodology. Contained within this dissertation is an original methodology that permits the aforementioned structure-based iv dendrogram generation hypothesis. Additionally, I have scripted three novel bioinformatics programs required by this proposed methodology: a protein structure alignment program that proficiently superimposes distant homologs, an accurate structure-dependent sequence alignment program, and a dendrogram generation program that employs a novel structural molecular clock hypothesis. The results from this methodology support the proposed hypothesis by demonstrating that generating dendrograms utilizing protein structures is superior to those generated utilizing exclusively protein sequences.
    Table of Contents
    Introduction -- Sable: Structural alignment by maximum likelihood -- UNITS: Universal true SDSA (Structure-dependent sequience alignment) -- Push: phlyogenetic tree using structural homology) -- Push discussion and general conclusion -- Generic sorting algorithm -- Template protein selection -- Units and chimera SDSAs -- References -- Vita
    URI
    https://hdl.handle.net/10355/45496
    Degree
    Ph.D.
    Thesis Department
    Molecular Biology and Biochemistry (UMKC)
     
    Cell Biology and Biophysics (UMKC)
     
    Collections
    • 2013 UMKC Dissertations - Freely Available Online
    • Cell Biology and Biophysics Electronic Theses and Dissertations (UMKC)
    • Molecular Biology and Biochemistry Electronic Theses and Dissertations (UMKC)

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