Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book An Introduction to Molecular Dynamics written by Mark S. Kemp and published by Nova Science Publishers. This book was released on 2019 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt: "In the opening chapter of An Introduction to Molecular Dynamics, the method of statistical geometry, based on the construction of a Voronoi polyhedral, is applied to the pattern recognition of atomic environments and to the investigation of the local order in molecular dynamics-simulated materials. Next, the authors discuss the methodology of bimolecular simulations and their advancements, as well as their applications in the field of nanoparticle-biomolecular interactions. The theory of molecular dynamics simulation and some of the recent molecular dynamics methods such as steered molecular dynamics, umbrella sampling, and coarse-grained simulation are also discussed. The use of auxiliary programs in the cases of modified cyclodextrins is discussed. Additionally, results from molecular dynamics studies on cases of inclusion compounds of molecules of different sizes and shapes encapsulated in the same host cyclodextrin have been examined and compared. In closing, the authors discuss the methodology of molecular dynamics simulation with a non-constant force field. In the context of molecular simulations, the term "force field" refers to a set of equations and parameters for the calculation of forces acting on the particles of the system and its potential energy"--
Download or read book Protein Dynamics written by Dennis R. Livesay and published by Humana. This book was released on 2016-08-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Computational Biochemistry and Biophysics written by Oren M. Becker and published by CRC Press. This book was released on 2001-02-09 with total page 534 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covering theoretical methods and computational techniques in biomolecular research, this book focuses on approaches for the treatment of macromolecules, including proteins, nucleic acids, and bilayer membranes. It uses concepts in free energy calculations, conformational analysis, reaction rates, and transition pathways to calculate and interpret b
Download or read book Simulating Protein Dynamics written by V. Vishal and published by . This book was released on 2007 with total page 168 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Free Energy Calculations written by Christophe Chipot and published by Springer Science & Business Media. This book was released on 2007-01-08 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.
Download or read book Protein Engineering written by Uwe T. Bornscheuer and published by Humana Press. This book was released on 2017-10-30 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details basic and advanced protocols for both stages of protein engineering: the library design phase and the identification of improved variants by screening and selection. Chapters focus on enzyme engineering using rational and semi-rational approaches. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Protein Engineering: Methods and Protocols aims to aid scientists in the planning and performance of their experiments. The chapter 'Functional Analysis of Membrane Proteins Produced by Cell-Free Translation' is open access under a CC BY 4.0 license via link.springer.com.
Download or read book Molecular Modeling of Proteins written by Andreas Kukol and published by Humana Press. This book was released on 2017-04-30 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions and notes on troubleshooting and avoiding common pitfalls. Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical and biosciences interested in utilizing this powerful technology.
Download or read book Protein Engineering and Design written by Paul R. Carey and published by Elsevier. This book was released on 1996-06-21 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: The design and production of novel peptides and proteins occupy pivotal positions in science and technology and will continue to do so in the 21st century. Protein Engineering and Design outlines the rapid advances in computer-based modeling, protein engineering, and methods needed for protein and peptide preparation and characterization. This indispensable reference lays the groundwork for understanding this multidisciplinary activity while providing an introduction for researchers and students to the field of protein design. - Introduces and defines the techniques involved in protein engineering and design - Provides a concise overview of key technologies involved and demonstrates their contributions to the specialized design and production of novel proteins and peptides
Download or read book The Art of Molecular Dynamics Simulation written by D. C. Rapaport and published by Cambridge University Press. This book was released on 2004-04 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt: First time paperback of successful physics monograph. Copyright © Libri GmbH. All rights reserved.
Download or read book Protein nucleic Acid Interaction written by Wolfram Saenger and published by . This book was released on 1989 with total page 230 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains a series of essays which describe a range of problems in the field of nucleic-acid interactions, investigated by a variety of techniques. An introductory chapter on DNA-protein interactions in the regulation of gene expression is followed by papers on selected model systems.
Download or read book Biomolecular Simulations written by Massimiliano Bonomi and published by Humana. This book was released on 2020-08-14 with total page 581 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; Part Two discusses enhanced sampling and free-energy calculations; Part Three talks about integrative computational and experimental approaches for biomolecular simulations; and Part Four focuses on analyzing, visualizing, and comparing biomolecular simulations. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Biomolecular Simulations: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in studying different areas of biomolecular simulations, and discovering new tools to progress their future projects.
Download or read book Protein Actions Principles and Modeling written by Ivet Bahar and published by Garland Science. This book was released on 2017-02-14 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Actions: Principles and Modeling is aimed at graduates, advanced undergraduates, and any professional who seeks an introduction to the biological, chemical, and physical properties of proteins. Broadly accessible to biophysicists and biochemists, it will be particularly useful to student and professional structural biologists and molecular biophysicists, bioinformaticians and computational biologists, biological chemists (particularly drug designers) and molecular bioengineers. The book begins by introducing the basic principles of protein structure and function. Some readers will be familiar with aspects of this, but the authors build up a more quantitative approach than their competitors. Emphasizing concepts and theory rather than experimental techniques, the book shows how proteins can be analyzed using the disciplines of elementary statistical mechanics, energetics, and kinetics. These chapters illuminate how proteins attain biologically active states and the properties of those states. The book ends with a synopsis the roles of computational biology and bioinformatics in protein science.
Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. - Presents a thorough overview of the latest and emerging methods and technologies for protein study - Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy - Includes computational and machine learning methods - Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins
Download or read book Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio Lammps and Gromacs written by Sumit Sharma and published by Elsevier. This book was released on 2019-08-09 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs presents the three major software packages used for the molecular dynamics simulation of nanocomposites. The book explains, in detail, how to use each of these packages, also providing real-world examples that show when each should be used. The latter two of these are open-source codes which can be used for modeling at no cost. Several case studies how each software package is used to predict various properties of nanocomposites, including metal-matrix, polymer-matrix and ceramic-matrix based nanocomposites. Properties explored include mechanical, thermal, optical and electrical properties. This is the first book that explores methodologies for using Materials Studio, Lammps and Gromacs in the same place. It will be beneficial for students, researchers and scientists working in the field of molecular dynamics simulation. - Gives a detailed explanation of basic commands and modules of Materials Studio, Lammps and Gromacs - Shows how Materials Studio, Lammps and Gromacs predict mechanical, thermal, electrical and optical properties of nanocomposites - Uses case studies to show which software should be used to solve a variety of nanoscale modeling problems
Download or read book Computational Approaches to Protein Dynamics written by Monika Fuxreiter and published by CRC Press. This book was released on 2014-12-24 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Molecular Simulations and Biomembranes written by Mark S P Sansom and published by Royal Society of Chemistry. This book was released on 2010-08-01 with total page 331 pages. Available in PDF, EPUB and Kindle. Book excerpt: The need for information in the understanding of membrane systems has been caused by three things - an increase in computer power; methodological developments and the recent expansion in the number of researchers working on it worldwide. However, there has been no up-to-date book that covers the application of simulation methods to membrane systems directly and this book fills an important void in the market. It provides a much needed update on the current methods and applications as well as highlighting recent advances in the way computer simulation can be applied to the field of membranes and membrane proteins. The objectives are to show how simulation methods can provide an important contribution to the understanding of these systems. The scope of the book is such that it covers simulation of membranes and membrane proteins, but also covers the more recent methodological developments such as coarse-grained molecular dynamics and multiscale approaches in systems biology. Applications embrace a range of biological processes including ion channel and transport proteins. The book is wide ranging with broad coverage and a strong coupling to experimental results wherever possible, including colour illustrations to highlight particular aspects of molecular structure. With an internationally respected list of authors, its publication is timely and it will prove indispensable to a large scientific readership.
