Titlebook: Biomolecules‘ Conformational Changes Studied by Simulations and Enhanced Sampling; Yui Tik (Andrew) Pang Book 2024 The Editor(s) (if appli

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Book 2024molecular behavior across various scales. Furthermore, the thesis advances the field by updating the Force Field Toolkit for improved simulation accuracy. This work not only showcases the adaptability and importance of simulation techniques in modern biological research but also paves the way for no

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Biomolecules‘ Conformational Changes Studied by Simulations and Enhanced Sampling

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Parameterization of a Drug Molecule with a Halogen ,-Hole Particle Using ffTK: Implementation, TestfTK, an automated force field parameterization toolkit widely distributed as a plugin to the molecular visualization software VMD. We demonstrate the updated optimization process using an example halogenated drug molecule, AT130, which is a capsid assembly modulator targeting the hepatitis B virus.

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Uncovering the Folding Mechanism of Pertactin: A Comparative Study of Isolated and Vectorial Foldin (“isolated folding”) versus folding rungs on top of a previously folded rung (“vectorial folding”). Our results showed that vectorial folding is highly favorable compared with isolated folding; moreover, our simulations showed that the C-terminal rung of the β-helix is the most resistant to unfoldi

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SARS-CoV-2 Spike Opening Dynamics and Energetics Reveal the Individual Roles of Glycans and Their Citope exposure for several known antibodies changes along the opening path. We find that the BD-368-2 antibody’s epitope is continuously exposed, explaining its high efficacy. Reproduced with permission from Pang, Y. T.; Acharya, A.; Lynch, D. L.; Pavlova, A.; Gumbart, J. C. “SARS-CoV-2 spike openin

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2190-5053 dating the Force Field Toolkit for improved simulation accuracy. This work not only showcases the adaptability and importance of simulation techniques in modern biological research but also paves the way for no978-3-031-70604-2978-3-031-70602-8Series ISSN 2190-5053 Series E-ISSN 2190-5061