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Biomolecules' conformational changes studied by simulations and enhanced sampling

Record Type:	Electronic resources : Monograph/item
Title/Author:	Biomolecules' conformational changes studied by simulations and enhanced samplingby Yui Tik (Andrew) Pang.
Author:	Pang, Yui Tik.
Published:	Cham :Springer Nature Switzerland :2024.
Description:	xiv, 97 p. :ill. (some col.), digital ;24 cm.
Notes:	"Doctoral thesis accepted by Georgia Institute of Technology, USA."
Contained By:	Springer Nature eBook
Subject:	Biomolecules.
Online resource:	https://doi.org/10.1007/978-3-031-70602-8
ISBN:	9783031706028$q(electronic bk.)

Biomolecules' conformational changes studied by simulations and enhanced sampling
Pang, Yui Tik.

Biomolecules' conformational changes studied by simulations and enhanced sampling[electronic resource] /by Yui Tik (Andrew) Pang. - Cham :Springer Nature Switzerland :2024. - xiv, 97 p. :ill. (some col.), digital ;24 cm. - Springer theses,2190-5061. - Springer theses..

"Doctoral thesis accepted by Georgia Institute of Technology, USA."

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.

ISBN: 9783031706028$q(electronic bk.)

Standard No.: 10.1007/978-3-031-70602-8doiSubjects--Topical Terms:

194433
Biomolecules.

LC Class. No.: QP514.2

Dewey Class. No.: 572

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520 $a 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.
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