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Author: Monika Fuxreiter
Publisher: CRC Press
ISBN: 1482297868
Category : Science
Languages : en
Pages : 458
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Book Description
The Latest Developments on the Role of Dynamics in Protein FunctionsComputational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, an
Author: Monika Fuxreiter
Publisher: CRC Press
ISBN: 1482297868
Category : Science
Languages : en
Pages : 458
Get Book Here
Book Description
The Latest Developments on the Role of Dynamics in Protein FunctionsComputational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, an
Author:
Publisher: Academic Press
ISBN: 0128211377
Category : Science
Languages : en
Pages : 554
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Book Description
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. Includes comprehensive coverage on molecular biology Presents ample use of tables, diagrams, schemata and color figures to enhance the reader's ability to rapidly grasp the information provided Contains contributions from renowned experts in the field
Author:
Publisher:
ISBN:
Category :
Languages : en
Pages : 192
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Book Description
Author: Dennis R. Livesay
Publisher: Humana
ISBN: 9781493963072
Category : Science
Languages : en
Pages : 0
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Book Description
In Protein Dynamics: Methods and Protocols, expert researchers in the field detail both experimental and computational methods to interrogate molecular level fluctuations. Chapters detail best-practice recipes covering both experimental and computational techniques, reflecting modern protein research. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein Dynamics: Methods and Protocols describes the most common and powerful methods used to characterize protein dynamics.
Author: Tobias Sikosek
Publisher: Humana
ISBN: 9781493987351
Category : Science
Languages : en
Pages : 0
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Book Description
This volume presents a diverse collection of methodologies used to study various problems at the protein sequence and structure level. The chapters in this book look at issues ranging from broad concepts like protein space to specifics like antibody modeling. Topics include point mutations, gene duplication, de novo emergence of new genes, pairwise correlated mutations, ancestral protein reconstruction, homology modelling, protein stability and dynamics, and protein-protein interactions. The book also covers a wide range of computational approaches, including sequence and structure alignments, phylogenies, physics-based and mathematical approaches, machine learning, and more. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and prerequisites, step-by-step, readily reproducible computational protocols (using command line or graphical user interfaces, sometimes including computer code), and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Computational Methods in Protein Evolution is a valuable resource that offers useful workflows and techniques that will help both novice and expert researchers working with proteins computationally.
Author: Ke-li Han
Publisher: Springer Science & Business Media
ISBN: 3319029703
Category : Medical
Languages : en
Pages : 488
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Book Description
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.
Author: Andrzej Kolinski
Publisher: Springer Science & Business Media
ISBN: 144196889X
Category : Science
Languages : en
Pages : 360
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Book Description
The book gives a comprehensive review of the most advanced multiscale methods for protein structure prediction, computational studies of protein dynamics, folding mechanisms and macromolecular interactions. It approaches span a wide range of the levels of coarse-grained representations, various sampling techniques and variety of applications to biomedical and biophysical problems. This book is intended to be used as a reference book for those who are just beginning their adventure with biomacromolecular modeling but also as a valuable source of detailed information for those who are already experts in the field of biomacromolecular modeling and in related areas of computational biology or biophysics.
Author:
Publisher:
ISBN:
Category :
Languages : en
Pages : 528
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Book Description
The "protein structure-function" paradigm, which states that proteins adopt nearly rigid 3-dimensional structures that are responsible for their function, is one of the central tenets of molecular biology, yet some proteins and protein domains exist as intrinsically disordered forms. In this dissertation, new approaches to define a metric for the dynamics of disordered proteins are developed which are also readily applicable to the study of non-equilibrium globular protein dynamics. First, standard metrics for comparing protein dynamics are applied to molecular dynamics (MD) simulations of a class of entirely disordered proteins (outside of a small anchoring domain) involved in nucleocytoplasmic transport, the FG-nucleoporins (FG-Nups). After this, clustering and dimensionality reduction techniques are utilized to reveal previously unknown characteristics regarding the convergence properties of disordered protein simulations. Next, the novel application of polymer models is used to assess the efficacy of clustering and dimensionality estimation algorithms applied to MD trajectories. Finally, the results are used to analyze the differences between FG-Nup dynamics and the dynamics of two fast-folding globular proteins, GB1 and Trp-cage. The results indicate that polymer models are an effective tool for validating computational techniques for studying protein simulations, and that the various proteins can be classified by differences in their underlying dynamics
Author: Prakash Saudagar
Publisher: Springer Nature
ISBN: 9819920795
Category : Science
Languages : en
Pages : 287
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Book Description
This book describes recent important advancements in protein folding dynamics and stability research, as well as explaining fundamentals and examining potential methodological approaches in protein science. In vitro, in silico, and in vivo method based research of how the stability and folding of proteins help regulate the cellular dynamics and impact cell function that are crucial in explaining various physiological and pathological processes. This book offers a comprehensive coverage on various techniques and related recent developments in the experimental and computational methods of protein folding, dynamics, and stability studies. The book is also structured in such a way as to summarize the latest developments in the fiddle and key concepts to ensure that readers can understand advanced concepts as well as the fundamental big picture. And most of all, fresh insights are provided into the convergence of protein science and technology. Protein Folding Dynamics and Stability is an ideal guide to the field that will be of value for all levels of researchers and advanced graduate students with training in biochemical laboratory research.
Author: Ilan Samish
Publisher: Humana
ISBN: 9781493966356
Category : Science
Languages : en
Pages : 0
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Book Description
The aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.
