04018nam a22006255i 4500 978-3-031-70602-8 DE-He213 20251030113109.0 cr nn 008mamaa 240927s2024 sz | s |||| 0|eng d 9783031706028 978-3-031-70602-8 10.1007/978-3-031-70602-8 doi QH505 PHVN bicssc SCI009000 bisacsh PHVN thema Pang, Yui Tik (Andrew). author. aut http://id.loc.gov/vocabulary/relators/aut 85105 Biomolecules' Conformational Changes Studied by Simulations and Enhanced Sampling [electronic resource] / by Yui Tik (Andrew) Pang. 1st ed. 2024. Cham : Springer Nature Switzerland : Imprint: Springer, 2024. XIV, 97 p. 38 illus., 36 illus. in color. online resource. text txt rdacontent computer c rdamedia online resource cr rdacarrier text file PDF rda Springer Theses, Recognizing Outstanding Ph.D. Research, 2190-5061 Chapter 1: Introduction and Background -- Chapter 2: Parameterization of a drug molecule with a halogen-hole particle using ffTK: Implementation, testing, and comparison -- Chapter 3: Uncovering the folding mechanism of pertactin: A comparative study of isolated and vectorial folding -- Chapter 4: SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact -- Chapter 5: Conclusions and Future Work. This thesis illuminates the critical roles biomolecules, from small molecules to proteins, play in cellular functionality, particularly highlighting their conformational changes in response to environmental cues or binding events—a cornerstone concept in drug design as well as the manifestations of disease. It explores the conformational flexibility of small molecules and proteins, essential for predicting drug interactions and understanding biological processes. Through advanced molecular dynamics simulations and enhanced sampling techniques, this research offers unprecedented insights into the structural dynamics of three distinct biomolecular systems: the capsid assembly modulator AT130, the passenger domain of pertactin, and the SARS-CoV-2 spike protein. Each system represents a unique facet of biological complexity, underscoring the thesis's contribution to our understanding of biomolecular 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 novel therapeutic strategies by deepening our understanding of biomolecular dynamics. Biophysics. 66239 Biomolecules. 66771 Mathematical physics. Computer simulation. Virology. 72539 Proteins. 70651 Biomaterials. Molecular biology. Molecular Biophysics. 66774 Computational Physics and Simulations. 65564 Virology. 72539 Biomaterials-Proteins. 71152 Molecular Biology. SpringerLink (Online service) Springer Nature eBook Printed edition: 9783031706011 Printed edition: 9783031706035 Printed edition: 9783031706042 Springer Theses, Recognizing Outstanding Ph.D. Research, 2190-5061 66370 https://doi.org/10.1007/978-3-031-70602-8 ZDB-2-PHA ZDB-2-SXP 63758 63758