Computational methods for the incorporation of protein unfolding pathways and kinetics in protein design
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Authors
Walcott, Benjamin David
Issue Date
2018-08
Type
Electronic thesis
Thesis
Thesis
Language
ENG
Keywords
Biology
Alternative Title
Abstract
Hydrophobic collapse is one of the main driving forces of protein folding. As such, accurately modeling solvation effects and electrostatics is a key component of any energy function. This can be achieved through explicitly modeling each solvent water molecule or by implicitly modeling the bulk solvent as a continuum. GeoFold utilizes a solvent accessible surface area (SAS) based implicit solvation model; however, it does not adequately capture the impact of exposure to solvent of hydrophobic vs hydrophilic residues. In this work, the WZS model is implemented, demonstrating improved accuracy in the prediction of unfolding rates in an 86-protein case study.
Description
August 2018
School of Science
School of Science
Full Citation
Publisher
Rensselaer Polytechnic Institute, Troy, NY