Modeling Protein Conformational Dynamics Using Kinetic Network Models
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Modeling Protein Conformational Dynamics Using Kinetic Network Models
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Author : Zhaoning Cui
language : en
Publisher:
Release Date : 2013
Modeling Protein Conformational Dynamics Using Kinetic Network Models written by Zhaoning Cui and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013 with Proteins categories.
Protein Conformational Dynamics
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Author : Ke-li Han
language : en
Publisher: Springer Science & Business Media
Release Date : 2014-01-20
Protein Conformational Dynamics written by Ke-li Han and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-01-20 with Medical categories.
This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.
Computational Approaches For Understanding Dynamical Systems Protein Folding And Assembly
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Author :
language : en
Publisher: Academic Press
Release Date : 2020-03-04
Computational Approaches For Understanding Dynamical Systems Protein Folding And Assembly written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-03-04 with Science categories.
Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, Volume 170 in the Progress in Molecular Biology and Translational Science series, provides the most topical, informative and exciting monographs available on a wide variety of research topics. The series includes in-depth knowledge on the molecular biological aspects of organismal physiology, with this release including chapters on Pairwise-Additive and Polarizable Atomistic Force Fields for Molecular Dynamics Simulations of Proteins, Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers, Enhanced sampling and free energy methods, and much more.
Advanced Sampling And Modeling In Molecular Simulations For Slow And Large Scale Biomolecular Dynamics
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Author : Xiakun Chu
language : en
Publisher: Frontiers Media SA
Release Date : 2022-01-07
Advanced Sampling And Modeling In Molecular Simulations For Slow And Large Scale Biomolecular Dynamics written by Xiakun Chu and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-01-07 with Science categories.
Biomolecular Simulations In Structure Based Drug Discovery
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Author : Francesco L. Gervasio
language : en
Publisher: John Wiley & Sons
Release Date : 2019-01-04
Biomolecular Simulations In Structure Based Drug Discovery written by Francesco L. Gervasio and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-01-04 with Medical categories.
A guide to applying the power of modern simulation tools to better drug design Biomolecular Simulations in Structure-based Drug Discovery offers an up-to-date and comprehensive review of modern simulation tools and their applications in real-life drug discovery, for better and quicker results in structure-based drug design. The authors describe common tools used in the biomolecular simulation of drugs and their targets and offer an analysis of the accuracy of the predictions. They also show how to integrate modeling with other experimental data. Filled with numerous case studies from different therapeutic fields, the book helps professionals to quickly adopt these new methods for their current projects. Experts from the pharmaceutical industry and academic institutions present real-life examples for important target classes such as GPCRs, ion channels and amyloids as well as for common challenges in structure-based drug discovery. Biomolecular Simulations in Structure-based Drug Discovery is an important resource that: -Contains a review of the current generation of biomolecular simulation tools that have the robustness and speed that allows them to be used as routine tools by non-specialists -Includes information on the novel methods and strategies for the modeling of drug-target interactions within the framework of real-life drug discovery and development -Offers numerous illustrative case studies from a wide-range of therapeutic fields -Presents an application-oriented reference that is ideal for those working in the various fields Written for medicinal chemists, professionals in the pharmaceutical industry, and pharmaceutical chemists, Biomolecular Simulations in Structure-based Drug Discovery is a comprehensive resource to modern simulation tools that complement and have the potential to complement or replace laboratory assays for better results in drug design.
Understanding Protein Dynamics Binding And Allostery For Drug Design
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Author : Guang Hu
language : en
Publisher: Frontiers Media SA
Release Date : 2021-06-08
Understanding Protein Dynamics Binding And Allostery For Drug Design written by Guang Hu and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-06-08 with Science categories.
Primate Lentiviruses Advances In Research And Application 2012 Edition
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Author :
language : en
Publisher: ScholarlyEditions
Release Date : 2012-12-26
Primate Lentiviruses Advances In Research And Application 2012 Edition written by and has been published by ScholarlyEditions this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-12-26 with Medical categories.
Primate Lentiviruses—Advances in Research and Application: 2012 Edition is a ScholarlyEditions™ eBook that delivers timely, authoritative, and comprehensive information about Primate Lentiviruses. The editors have built Primate Lentiviruses—Advances in Research and Application: 2012 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Primate Lentiviruses in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of Primate Lentiviruses—Advances in Research and Application: 2012 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.
Markov State Models For Protein And Rna Folding
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Author : Gregory Ross Bowman
language : en
Publisher: Stanford University
Release Date : 2010
Markov State Models For Protein And Rna Folding written by Gregory Ross Bowman and has been published by Stanford University this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.
Understanding the molecular bases of human health could greatly augment our ability to prevent and treat diseases. For example, a deeper understanding of protein folding would serve as a reference point for understanding, preventing, and reversing protein misfolding in diseases like Alzheimer's. Unfortunately, the small size and tremendous flexibility of proteins and other biomolecules make it difficult to simultaneously monitor their thermodynamics and kinetics with sufficient chemical detail. Atomistic Molecular Dynamics (MD) simulations can provide a solution to this problem in some cases; however, they are often too short to capture biologically relevant timescales with sufficient statistical accuracy. We have developed a number of methods to address these limitations. In particular, our work on Markov State Models (MSMs) now makes it possible to map out the conformational space of biomolecules by combining many short simulations into a single statistical model. Here we describe our use of MSMs to better understand protein and RNA folding. We chose to focus on these folding problems because of their relevance to misfolding diseases and the fact that any method capable of describing such drastic conformational changes should also be applicable to less dramatic but equally important structural rearrangements like allostery. One of the key insights from our folding simulations is that protein native states are kinetic hubs. That is, the unfolded ensemble is not one rapidly mixing set of conformations. Instead, there are many non-native states that can each interconvert more rapidly with the native state than with one another. In addition to these general observations, we also demonstrate how MSMs can be used to make predictions about the structural and kinetic properties of specific systems. Finally, we explain how MSMs and other enhanced sampling algorithms can be used to drive efficient sampling.
Nuclear Magnetic Resonance
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Author : Krystyna Kamienska-Trela
language : en
Publisher: Royal Society of Chemistry
Release Date : 2015-05-20
Nuclear Magnetic Resonance written by Krystyna Kamienska-Trela and has been published by Royal Society of Chemistry this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-05-20 with Science categories.
Applications of nuclear magnetic resonance span a wide range of scientific disciplines, from physics to medicine. This series has provided an essential digest of the NMR literature for more than four decades and each volume provides unrivalled coverage of the literature on this topic. Continuous coverage on some topics such as theoretical and physical aspects of nuclear shielding is balance by the desire for coverage on newer topics like applications in biological systems and materials science. For those wanting to become rapidly acquainted with NMR or seasoned practitioners, this is an invaluable source of current methods and applications.
Integrating Timescales From Molecules Up
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Author : Rene A. Nome
language : en
Publisher: Frontiers Media SA
Release Date : 2021-06-04
Integrating Timescales From Molecules Up written by Rene A. Nome and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-06-04 with Science categories.