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Development of the fast analysis suite and its implementation on analysis of MHC class I proteins and KRAS
Heikes, Micah E.
Heikes, Micah E.
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t24012_Heikes.pdf
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2024-05
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This thesis introduces the "Fast Analysis Suite," a novel computational tool designed to revolutionize the analysis of protein structures and dynamics. The suite comprises two main applications: a Structure Analysis Suite and a Bash Script Generator for GROMACS simulations. The Structure Analysis Suite provides comprehensive insights into protein structures, detailing secondary structures, amino acid properties, and solvent accessible surface areas, which are essential for understanding protein functionality and interactions. The Bash Script Generator automates the creation of scripts necessary for advanced molecular dynamics analyses, such as characterizing the biomolecular solvation layer by calculating Diffusion Coefficients, Reorientation Times, Hydrogen Bond Lifetimes, and Radial Distribution Functions, thereby significantly reducing manual scripting efforts and potential errors. The effectiveness and efficiency of this suite are demonstrated through simulations on two biologically significant proteins: MHC Class 1 proteins, which play a critical role in the immune response, and KRAS, a key protein often implicated in cancer development due to its mutational propensity. The results showcase the suite's ability to provide fast, accurate, and comprehensive analyses, highlighting its potential as a valuable tool in protein research and its contribution to the fields of computational biology and molecular biophysics. This work not only presents a significant advancement in the methodology of protein analysis but also paves the way for accelerated discoveries related to hydration dynamics and protein function.
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Thesis (M.S.)-- Wichita State University, College of Liberal Arts and Sciences, Dept. of Chemistry and Biochemistry
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Wichita State University
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© Copyright 2024 by Micah E. Heikes
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