03643nam a22005415i 4500001001800000003000900018005001700027007001500044008004100059020001800100024003500118050001000153072001700163072002300180072001600203100008500219245013800304250001800442264006900460300006400529336002600593337002600619338003600645347002400681490007200705505046200777520128901239650001602528650001802544650002602562650002502588650001402613650001402627650001802641650002302659650002602682650004302708650001402751650002702765650002302792710003402815773002602849776003602875776003602911776003602947830007202983856004603055978-3-031-70602-8DE-He21320251030113109.0cr nn 008mamaa240927s2024    sz |    s    |||| 0|eng d  a97830317060287 a10.1007/978-3-031-70602-82doi 4aQH505 7aPHVN2bicssc 7aSCI0090002bisacsh 7aPHVN2thema1 aPang, Yui Tik (Andrew).eauthor.4aut4http://id.loc.gov/vocabulary/relators/aut10aBiomolecules' Conformational Changes Studied by Simulations and Enhanced Samplingh[electronic resource] /cby Yui Tik (Andrew) Pang.  a1st ed. 2024. 1aCham :bSpringer Nature Switzerland :bImprint: Springer,c2024.  aXIV, 97 p. 38 illus., 36 illus. in color.bonline resource.  atextbtxt2rdacontent  acomputerbc2rdamedia  aonline resourcebcr2rdacarrier  atext filebPDF2rda1 aSpringer Theses, Recognizing Outstanding Ph.D. Research,x2190-50610 aChapter 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.  aThis 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. 0aBiophysics. 0aBiomolecules. 0aMathematical physics. 0aComputer simulation. 0aVirology. 0aProteins. 0aBiomaterials. 0aMolecular biology.14aMolecular Biophysics.24aComputational Physics and Simulations.24aVirology.24aBiomaterials-Proteins.24aMolecular Biology.2 aSpringerLink (Online service)0 tSpringer Nature eBook08iPrinted edition:z978303170601108iPrinted edition:z978303170603508iPrinted edition:z9783031706042 0aSpringer Theses, Recognizing Outstanding Ph.D. Research,x2190-506140uhttps://doi.org/10.1007/978-3-031-70602-8