CHBC Faculty Publications

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Author: Ogden, Dylan Sebastien

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TitlePublication NamePub. TypeYear
Atomic-level characterization of the conformational transition pathways in SARS-CoV-1 and SARS-CoV-2 spike proteinsbioRxivJournal Article2022
Prefusion spike protein conformational changes are slower in SARS-CoV-2 than in SARS-CoV-1Journal of Biological ChemistryJournal Article2022
A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and PitfallsJournal of Chemical Theory and ComputationJournal Article2022
Molecular Dynamics-Based Thermodynamic and Kinetic Characterization of Membrane Protein Conformational Transitions.Structure and Function of Membrane ProteinsBook Section2021
Conformational free energy landscape of prefusion spike protein in SARS-CoV-1 and 2.Abstracts of Papers of the American Chemical SocietyAbstract2021
Similarities and differences of conformational transition pathways in uniporters, symporters, and antiporters of the major facilitator superfamily of transporters.Abstracts of Papers of the American Chemical SocietyAbstract2021
Differential thermodynamics and kinetics of prefusion spike proteins of SARS-CoV-1 and 2.Abstracts of Papers of the American Chemical SocietyAbstract2021
Conformational Transition Pathway of GkPOTBiophysical JournalAbstract2021
Differential Dynamic Behavior of Prefusion Spike Glycoproteins of Sars Coronaviruses 1 and 2Biophysical JournalAbstract2021
An Investigation of the Conformational Dynamics of ABC Exporter PCAT1 using Microsecond-Level MD SimulationsBiophysical JournalAbstract2021
An Investigation of the Influenza Hemagglutinin Membrane Fusion Process using Microsecond-Level MD SimulationsBiophysical JournalAbstract2020
Differential dynamic behavior of prefusion spike proteins of SARS coronaviruses 1 and 2bioRxivJournal Article2020
Binding Free Energy Calculations of NMDA Glutamate ReceptorsBiophysical JournalAbstract2019
Mechanistic Study of a Peptidase Containing ABC-Transporter, Employing Microsecond Level Molecular Dynamics Simulations and Enhanced Sampling TechniquesBiophysical JournalAbstract2019