Biomolecules' Conformational Changes Studied by Simulations and Enhanced Sampling
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...
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| Format: | Electronic eBook |
| Language: | English |
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Cham :
Springer Nature Switzerland : Imprint: Springer,
2024.
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| Edition: | 1st ed. 2024. |
| Series: | Springer Theses, Recognizing Outstanding Ph.D. Research,
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| Online Access: | https://doi.org/10.1007/978-3-031-70602-8 |
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| 100 | 1 | |a Pang, Yui Tik (Andrew). |e author. |0 (orcid)0000-0003-4843-4468 |1 https://orcid.org/0000-0003-4843-4468 |4 aut |4 http://id.loc.gov/vocabulary/relators/aut | |
| 245 | 1 | 0 | |a Biomolecules' Conformational Changes Studied by Simulations and Enhanced Sampling |h [electronic resource] / |c by Yui Tik (Andrew) Pang. |
| 250 | |a 1st ed. 2024. | ||
| 264 | 1 | |a Cham : |b Springer Nature Switzerland : |b Imprint: Springer, |c 2024. | |
| 300 | |a XIV, 97 p. 38 illus., 36 illus. in color. |b online resource. | ||
| 336 | |a text |b txt |2 rdacontent | ||
| 337 | |a computer |b c |2 rdamedia | ||
| 338 | |a online resource |b cr |2 rdacarrier | ||
| 341 | 0 | |b Table of contents navigation |2 onix | |
| 341 | 0 | |b Single logical reading order |2 onix | |
| 341 | 0 | |b Short alternative textual descriptions |2 onix | |
| 341 | 0 | |b Use of color is not sole means of conveying information |2 onix | |
| 341 | 0 | |b Use of high contrast between text and background color |2 onix | |
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| 341 | 0 | |b All non-decorative content supports reading without sight |2 onix | |
| 347 | |a text file |b PDF |2 rda | ||
| 490 | 1 | |a Springer Theses, Recognizing Outstanding Ph.D. Research, |x 2190-5061 | |
| 505 | 0 | |a 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. | |
| 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. | ||
| 532 | 8 | |a Accessibility summary: This PDF does not fully comply with PDF/UA standards, but does feature limited screen reader support, described non-text content (images, graphs), bookmarks for easy navigation and searchable, selectable text. Users of assistive technologies may experience difficulty navigating or interpreting content in this document. We recognize the importance of accessibility, and we welcome queries about accessibility for any of our products. If you have a question or an access need, please get in touch with us at accessibilitysupport@springernature.com. | |
| 532 | 8 | |a No reading system accessibility options actively disabled | |
| 532 | 8 | |a Publisher contact for further accessibility information: accessibilitysupport@springernature.com | |
| 650 | 0 | |a Biophysics. | |
| 650 | 0 | |a Biomolecules. | |
| 650 | 0 | |a Mathematical physics. | |
| 650 | 0 | |a Computer simulation. | |
| 650 | 0 | |a Virology. | |
| 650 | 0 | |a Proteins. | |
| 650 | 0 | |a Biomaterials. | |
| 650 | 0 | |a Molecular biology. | |
| 650 | 1 | 4 | |a Molecular Biophysics. |
| 650 | 2 | 4 | |a Computational Physics and Simulations. |
| 650 | 2 | 4 | |a Virology. |
| 650 | 2 | 4 | |a Biomaterials-Proteins. |
| 650 | 2 | 4 | |a Molecular Biology. |
| 710 | 2 | |a SpringerLink (Online service) | |
| 773 | 0 | |t Springer Nature eBook | |
| 776 | 0 | 8 | |i Printed edition: |z 9783031706011 |
| 776 | 0 | 8 | |i Printed edition: |z 9783031706035 |
| 776 | 0 | 8 | |i Printed edition: |z 9783031706042 |
| 830 | 0 | |a Springer Theses, Recognizing Outstanding Ph.D. Research, |x 2190-5061 | |
| 856 | 4 | 0 | |u https://doi.org/10.1007/978-3-031-70602-8 |
| 912 | |a ZDB-2-PHA | ||
| 912 | |a ZDB-2-SXP | ||
| 950 | |a Physics and Astronomy (SpringerNature-11651) | ||
| 950 | |a Physics and Astronomy (R0) (SpringerNature-43715) | ||