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Molecular Dynamics Simulations Of Peptide And Protein Folding
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Book Synopsis Protein Simulations by : Valerie Daggett
Download or read book Protein Simulations written by Valerie Daggett and published by Elsevier. This book was released on 2003-11-26 with total page 477 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function.* Force Fields* Ligand Binding* Protein Membrane Simulation* Enzyme Dynamics* Protein Folding and unfolding simulations
Book Synopsis Molecular Modelling: Principles And Applications, 2/E by : Leach
Download or read book Molecular Modelling: Principles And Applications, 2/E written by Leach and published by Pearson Education India. This book was released on 2009-09 with total page 788 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Biomolecular Simulation by : Wilfred F. van Gunsteren
Download or read book Biomolecular Simulation written by Wilfred F. van Gunsteren and published by . This book was released on 1996 with total page 757 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computer Applications -- Physical Sciences and Engineering.
Book Synopsis Protein Folding Protocols by : Yawen Bai
Download or read book Protein Folding Protocols written by Yawen Bai and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covering experiment and theory, bioinformatics approaches, and state-of-the-art simulation protocols for better sampling of the conformational space, this volume describes a broad range of techniques to study, predict, and analyze the protein folding process. Protein Folding Protocols also provides sample approaches toward the prediction of protein structure starting from the amino acid sequence, in the absence of overall homologous sequences.
Book Synopsis Free Energy Calculations by : Christophe Chipot
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.
Book Synopsis Coarse-Grained Modeling of Biomolecules by : Garegin A. Papoian
Download or read book Coarse-Grained Modeling of Biomolecules written by Garegin A. Papoian and published by CRC Press. This book was released on 2017-10-30 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt: "The chapters in this book survey the progress in simulating biomolecular dynamics.... The images conjured up by this work are not yet universally loved, but are beginning to bring new insights into the study of biological structure and function. The future will decide whether this scientific movement can bring forth its Picasso or Modigliani." –from the Foreword by Peter G. Wolynes, Bullard-Welch Foundation Professor of Science, Rice University This book highlights the state-of-art in coarse-grained modeling of biomolecules, covering both fundamentals as well as various cutting edge applications. Coarse-graining of biomolecules is an area of rapid advances, with numerous new force fields having appeared recently and significant progress made in developing a systematic theory of coarse-graining. The contents start with first fundamental principles based on physics, then survey specific state-of-art coarse-grained force fields of proteins and nucleic acids, and provide examples of exciting biological problems that are at large scale, and hence, only amenable to coarse-grained modeling. Introduces coarse-grained models of proteins and nucleic acids. Showcases applications such as genome packaging in nuclei and understanding ribosome dynamics Gives the physical foundations of coarse-graining Demonstrates use of models for large-scale assemblies in modern studies Garegin A. Papoian is the first Monroe Martin Associate Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology at the University of Maryland.
Book Synopsis Dynamics of Proteins and Nucleic Acids by :
Download or read book Dynamics of Proteins and Nucleic Acids written by and published by Elsevier. This book was released on 2013-08-14 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Published continuously since 1944, Advances in Protein Chemistry and Structural Biology has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. - Covers reviews of methodology and research in all aspects of protein chemistry - Brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics
Download or read book Peptides written by Bernd Gutte and published by Elsevier. This book was released on 1995-10-24 with total page 527 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, research has shown the importance of peptides in neuroscience, immunology, and cell biology. Active research programs worldwide are now engaged in developing peptide-based drugs and vaccines using modification of natural peptides and proteins, design of artificial peptides and peptide mimetics, and screening of peptide and phage libraries. In this comprehensive book, the authors discuss peptide synthesis and application within the context of their increasing importance to the pharmaceutical industry. Peptides: Synthesis, Structures, and Applications explores the broad growth of information in modern peptide synthetic methods and the structure-activity relationships of synthetic polypeptides. - The history of peptide chemistry - Amide formation, deprotection, and disulfide formation in peptide synthesis - Solid-phase peptide synthesis - a-helix formation by peptides in water - Stability and dynamics of peptide conformation - An overview of structure-function studies of peptide hormones - Neuropeptides:peptide and nonpeptide analogs - Reversible inhibitors of serine proteinases - Design of polypeptides - Current capabilities and future possibilities of soluble chemical combinatorial libraries - Epitope mapping with peptides - Synthesis and applications of branched peptides in immunological methods and vaccines
Book Synopsis High Performance Computing in Science and Engineering, Garching/Munich 2007 by : Siegfried Wagner
Download or read book High Performance Computing in Science and Engineering, Garching/Munich 2007 written by Siegfried Wagner and published by Springer Science & Business Media. This book was released on 2008-10-22 with total page 700 pages. Available in PDF, EPUB and Kindle. Book excerpt: For the fourth time, the Leibniz Supercomputing Centre (LRZ) and the Com- tence Network for Technical, Scienti c High Performance Computing in Bavaria (KONWIHR) publishes the results from scienti c projects conducted on the c- puter systems HLRB I and II (High Performance Computer in Bavaria). This book reports the research carried out on the HLRB systems within the last three years and compiles the proceedings of the Third Joint HLRB and KONWIHR Result and Reviewing Workshop (3rd and 4th December 2007) in Garching. In 2000, HLRB I was the rst system in Europe that was capable of performing more than one Tera op/s or one billion oating point operations per second. In 2006 it was replaced by HLRB II. After a substantial upgrade it now achieves a peak performance of more than 62 Tera op/s. To install and operate this powerful system, LRZ had to move to its new facilities in Garching. However, the situation regarding the need for more computation cycles has not changed much since 2000. The demand for higher performance is still present, a trend that is likely to continue for the foreseeable future. Other resources like memory and disk space are currently in suf cient abundance on this new system.
Book Synopsis An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation by : Gregory R. Bowman
Download or read book An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation written by Gregory R. Bowman and published by Springer Science & Business Media. This book was released on 2013-12-02 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range of problems. The Markov state model (MSM) approach aims to address two key challenges of molecular simulation: 1) How to reach long timescales using short simulations of detailed molecular models. 2) How to systematically gain insight from the resulting sea of data. MSMs do this by providing a compact representation of the vast conformational space available to biomolecules by decomposing it into states sets of rapidly interconverting conformations and the rates of transitioning between states. This kinetic definition allows one to easily vary the temporal and spatial resolution of an MSM from high-resolution models capable of quantitative agreement with (or prediction of) experiment to low-resolution models that facilitate understanding. Additionally, MSMs facilitate the calculation of quantities that are difficult to obtain from more direct MD analyses, such as the ensemble of transition pathways. This book introduces the mathematical foundations of Markov models, how they can be used to analyze simulations and drive efficient simulations, and some of the insights these models have yielded in a variety of applications of molecular simulation.
Book Synopsis Computational Molecular Dynamics: Challenges, Methods, Ideas by : Peter Deuflhard
Download or read book Computational Molecular Dynamics: Challenges, Methods, Ideas written by Peter Deuflhard and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics. The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.
Book Synopsis Protein Conformational Dynamics by : Ke-li Han
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.
Book Synopsis Metastability and Markov State Models in Molecular Dynamics by : Christof Schütte
Download or read book Metastability and Markov State Models in Molecular Dynamics written by Christof Schütte and published by American Mathematical Soc.. This book was released on 2013-12-26 with total page 141 pages. Available in PDF, EPUB and Kindle. Book excerpt: Applications in modern biotechnology and molecular medicine often require simulation of biomolecular systems in atomic representation with immense length and timescales that are far beyond the capacity of computer power currently available. As a consequence, there is an increasing need for reduced models that describe the relevant dynamical properties while at the same time being less complex. In this book the authors exploit the existence of metastable sets for constructing such a reduced molecular dynamics model, the so-called Markov state model (MSM), with good approximation properties on the long timescales. With its many examples and illustrations, this book is addressed to graduate students, mathematicians, and practical computational scientists wanting an overview of the mathematical background for the ever-increasing research activity on how to construct MSMs for very different molecular systems ranging from peptides to proteins, from RNA to DNA, and via molecular sensors to molecular aggregation. This book bridges the gap between mathematical research on molecular dynamics and its practical use for realistic molecular systems by providing readers with tools for performing in-depth analysis of simulation and data-analysis methods. Titles in this series are co-published with the Courant Institute of Mathematical Sciences at New York University.
Book Synopsis Biomolecular and Bioanalytical Techniques by : Vasudevan Ramesh
Download or read book Biomolecular and Bioanalytical Techniques written by Vasudevan Ramesh and published by John Wiley & Sons. This book was released on 2019-06-10 with total page 576 pages. Available in PDF, EPUB and Kindle. Book excerpt: An essential guide to biomolecular and bioanalytical techniques and their applications Biomolecular and Bioanalytical Techniques offers an introduction to, and a basic understanding of, a wide range of biophysical techniques. The text takes an interdisciplinary approach with contributions from a panel of distinguished experts. With a focus on research, the text comprehensively covers a broad selection of topics drawn from contemporary research in the fields of chemistry and biology. Each of the internationally reputed authors has contributed a single chapter on a specific technique. The chapters cover the specific technique’s background, theory, principles, technique, methodology, protocol and applications. The text explores the use of a variety of analytical tools to characterise biological samples. The contributors explain how to identify and quantify biochemically important molecules, including small molecules as well as biological macromolecules such as enzymes, antibodies, proteins, peptides and nucleic acids. This book is filled with essential knowledge and explores the skills needed to carry out the research and development roles in academic and industrial laboratories. A technique-focused book that bridges the gap between an introductory text and a book on advanced research methods Provides the necessary background and skills needed to advance the research methods Features a structured approach within each chapter Demonstrates an interdisciplinary approach that serves to develop independent thinking Written for students in chemistry, biological, medical, pharmaceutical, forensic and biophysical sciences, Biomolecular and Bioanalytical Techniques is an in-depth review of the most current biomolecular and bioanalytical techniques in the field.
Book Synopsis Stochastic Dynamics by : Hans Crauel
Download or read book Stochastic Dynamics written by Hans Crauel and published by Springer Science & Business Media. This book was released on 2007-12-14 with total page 457 pages. Available in PDF, EPUB and Kindle. Book excerpt: Focusing on the mathematical description of stochastic dynamics in discrete as well as in continuous time, this book investigates such dynamical phenomena as perturbations, bifurcations and chaos. It also introduces new ideas for the exploration of infinite dimensional systems, in particular stochastic partial differential equations. Example applications are presented from biology, chemistry and engineering, while describing numerical treatments of stochastic systems.
Book Synopsis Protein Actions: Principles and Modeling by : Ivet Bahar
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.
