My PhD dissertation from Vanderbilt University (August 2021)
I completed my PhD research at Vanderbilt University from 2015-2021 in the laboratories of Jens Meiler and Hassane S. Mchaourab. This repository contains the source code for the entire dissertation, which was written in TeX at Overleaf. Everything was compiled with XeLaTeX. The templates files were designed by Eli Hooten, updated by Haley Adams, and made available by the University.
The contents are in the process of being published in scientific journals (last updated 7 May 2022):
- Chapter 1: Alternating access in LeuT-fold transporters (published in Journal of Molecular Biology)
- Chapter 2: Analysis and modelling applications of DEER data (unpublished)
- Chapter 3: Rapid simulation of unprocessed DEER decay data for protein fold prediction (published in Biophysical Journal)
- Chapter 4: Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints (published in Plos Computational Biology)
- Chapter 5:Structural dynamics of the glutamate-GABA antiporter GadC (published in Proceedings to the National Academy of Sciences)
- Chapter 6: Perspectives and future directions (unpublished)
- Appendix A: AlphaFold2 predicts the inward-facing conformation of the multidrug transporter LmrP (published in Proteins: Structure, Function, and Bioinformatics)
- Appendix B: Evaluation of scoring approaches for integrative modeling using DEER distance data (unpublished)
- Appendix C: Integrative modeling of conformational changes in LeuT-fold transporters using sparse spectroscopy data (published in Structure)
- Appendix D: Efficient sampling of loop conformations using conformational hashing and random coordinate descent (published in Journal of Chemical Theory and Computation)