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The Monte Carlo Approach To Biopolymers And Protein Folding

Author: Peter Grassberger

Publisher: World Scientific

Published: 1998-11-06

Total Pages: 346

ISBN-13: 9814544272

Information on our detailed genetic code is increasing at a dramatic pace. We need to understand how that is translated into the three-dimensional structure of proteins in order to make use of the information. Progress in this field is hampered by the lack of precise force fields and of efficient codes for finding equilibrium configurations of heteropolymers. However, there has been rapid advance in recent years, and this volume discusses that.

Computational Methods for Protein Folding, Volume 120

Author: Richard A. Friesner

Publisher: John Wiley & Sons

Published: 2004-04-07

Total Pages: 544

ISBN-13: 0471465232

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Since the first attempts to model proteins on a computer began almost thirty years ago, our understanding of protein structure and dynamics has dramatically increased. Spectroscopic measurement techniques continue to improve in resolution and sensitivity, allowing a wealth of information to be obtained with regard to the kinetics of protein folding and unfolding, and complementing the detailed structural picture of the folded state. Concurrently, algorithms, software, and computational hardware have progressed to the point where both structural and kinetic problems may be studied with a fair degree of realism. Despite these advances, many major challenges remain in understanding protein folding at both the conceptual and practical levels. Computational Methods for Protein Folding seeks to illuminate recent advances in computational modeling of protein folding in a way that will be useful to physicists, chemists, and chemical physicists. Covering a broad spectrum of computational methods and practices culled from a variety of research fields, the editors present a full range of models that, together, provide a thorough and current description of all aspects of protein folding. A valuable resource for both students and professionals in the field, the book will be of value both as a cutting-edge overview of existing information and as a catalyst for inspiring new studies. Computational Methods for Protein Folding is the 120th volume in the acclaimed series Advances in Chemical Physics, a compilation of scholarly works dedicated to the dissemination of contemporary advances in chemical physics, edited by Nobel Prize-winner Ilya Prigogine.

Current Topics in Computational Molecular Biology

Author: Tao Jiang

Publisher: MIT Press

Published: 2002

Total Pages: 570

ISBN-13: 9780262100922

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A survey of current topics in computational molecular biology. Computational molecular biology, or bioinformatics, draws on the disciplines of biology, mathematics, statistics, physics, chemistry, computer science, and engineering. It provides the computational support for functional genomics, which links the behavior of cells, organisms, and populations to the information encoded in the genomes, as well as for structural genomics. At the heart of all large-scale and high-throughput biotechnologies, it has a growing impact on health and medicine. This survey of computational molecular biology covers traditional topics such as protein structure modeling and sequence alignment, and more recent ones such as expression data analysis and comparative genomics. It combines algorithmic, statistical, database, and AI-based methods for studying biological problems. The book also contains an introductory chapter, as well as one on general statistical modeling and computational techniques in molecular biology. Each chapter presents a self-contained review of a specific subject. Not for sale in China, including Hong Kong.

Bayesian Methods in Structural Bioinformatics

Author: Thomas Hamelryck

Publisher: Springer

Published: 2012-03-23

Total Pages: 399

ISBN-13: 3642272258

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This book is an edited volume, the goal of which is to provide an overview of the current state-of-the-art in statistical methods applied to problems in structural bioinformatics (and in particular protein structure prediction, simulation, experimental structure determination and analysis). It focuses on statistical methods that have a clear interpretation in the framework of statistical physics, rather than ad hoc, black box methods based on neural networks or support vector machines. In addition, the emphasis is on methods that deal with biomolecular structure in atomic detail. The book is highly accessible, and only assumes background knowledge on protein structure, with a minimum of mathematical knowledge. Therefore, the book includes introductory chapters that contain a solid introduction to key topics such as Bayesian statistics and concepts in machine learning and statistical physics.

Handbook of Computational Chemistry

Author: Jerzy Leszczynski

Publisher: Springer Science & Business Media

Published: 2012-01-13

Total Pages: 1451

ISBN-13: 9400707118

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The role the Handbook of Computational Chemistry is threefold. It is primarily intended to be used as a guide that navigates the user through the plethora of computational methods currently in use; it explains their limitations and advantages; and it provides various examples of their important and varied applications. This reference work is presented in three volumes. Volume I introduces the different methods used in computational chemistry. Basic assumptions common to the majority of computational methods based on molecular, quantum, or statistical mechanics are outlined and special attention is paid to the limits of their applicability. Volume II portrays the applications of computational methods to model systems and discusses in detail molecular structures, the modelling of various properties of molecules and chemical reactions. Both ground and excited states properties are covered in the gas phase as well as in solution. This volume also describes Nanomaterials and covers topics such as clusters, periodic, and nano systems. Special emphasis is placed on the environmental effects of nanostructures. Volume III is devoted to the important class of Biomolecules. Useful models of biological systems considered by computational chemists are provided and RNA, DNA and proteins are discussed in detail. This volume presents examples of calcualtions of their properties and interactions and reveals the role of solvents in biologically important reactions as well as the structure function relationship of various classes of Biomolecules.

Energetics of Biological Macromolecules, Part E

Author:

Publisher: Elsevier

Published: 2004-04-02

Total Pages: 443

ISBN-13: 0080497187

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Energetics of Biological Macromolecules, Part E focuses on methods related to allosteric enzymes and receptors, including fluorescent proves, spectroscopic methods and quantitative analysis as well as on cooperativity in protein folding. NMR and mass spectrometry methods are discussed. Allosteric Enzymes and Receptors Cooperativity in Protein Folding and Assembly

Monte Carlo Methods in Chemical Physics

Author: David M. Ferguson

Publisher: John Wiley & Sons

Published: 2009-09-09

Total Pages: 576

ISBN-13: 0470142170

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In Monte Carlo Methods in Chemical Physics: An Introduction to the Monte Carlo Method for Particle Simulations J. Ilja Siepmann Random Number Generators for Parallel Applications Ashok Srinivasan, David M. Ceperley and Michael Mascagni Between Classical and Quantum Monte Carlo Methods: "Variational" QMC Dario Bressanini and Peter J. Reynolds Monte Carlo Eigenvalue Methods in Quantum Mechanics and Statistical Mechanics M. P. Nightingale and C.J. Umrigar Adaptive Path-Integral Monte Carlo Methods for Accurate Computation of Molecular Thermodynamic Properties Robert Q. Topper Monte Carlo Sampling for Classical Trajectory Simulations Gilles H. Peslherbe Haobin Wang and William L. Hase Monte Carlo Approaches to the Protein Folding Problem Jeffrey Skolnick and Andrzej Kolinski Entropy Sampling Monte Carlo for Polypeptides and Proteins Harold A. Scheraga and Minh-Hong Hao Macrostate Dissection of Thermodynamic Monte Carlo Integrals Bruce W. Church, Alex Ulitsky, and David Shalloway Simulated Annealing-Optimal Histogram Methods David M. Ferguson and David G. Garrett Monte Carlo Methods for Polymeric Systems Juan J. de Pablo and Fernando A. Escobedo Thermodynamic-Scaling Methods in Monte Carlo and Their Application to Phase Equilibria John Valleau Semigrand Canonical Monte Carlo Simulation: Integration Along Coexistence Lines David A. Kofke Monte Carlo Methods for Simulating Phase Equilibria of Complex Fluids J. Ilja Siepmann Reactive Canonical Monte Carlo J. Karl Johnson New Monte Carlo Algorithms for Classical Spin Systems G. T. Barkema and M.E.J. Newman

Reviews in Computational Chemistry, Volume 17

Author: Kenny B. Lipkowitz

Publisher: John Wiley & Sons

Published: 2003-05-08

Total Pages: 431

ISBN-13: 0471458813

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Computational chemistry is increasingly used in most areas of molecular science including organic, inorganic, medicinal, biological, physical, and analytical chemistry. Researchers in these fields who do molecular modelling need to understand and stay current with recent developments. This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Two chapters focus on molecular docking, one of which relates to drug discovery and cheminformatics and the other to proteomics. In addition, this volume contains tutorials on spin-orbit coupling and cellular automata modeling, as well as an extensive bibliography of computational chemistry books. FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."—JOURNAL OF MOLECULAR GRAPHICS AND MODELLING "One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."—JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Parallel Computing for Bioinformatics and Computational Biology

Author: Albert Y. Zomaya

Publisher: John Wiley & Sons

Published: 2006-04-21

Total Pages: 817

ISBN-13: 0471718483

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Discover how to streamline complex bioinformatics applications with parallel computing This publication enables readers to handle more complex bioinformatics applications and larger and richer data sets. As the editor clearly shows, using powerful parallel computing tools can lead to significant breakthroughs in deciphering genomes, understanding genetic disease, designing customized drug therapies, and understanding evolution. A broad range of bioinformatics applications is covered with demonstrations on how each one can be parallelized to improve performance and gain faster rates of computation. Current parallel computing techniques and technologies are examined, including distributed computing and grid computing. Readers are provided with a mixture of algorithms, experiments, and simulations that provide not only qualitative but also quantitative insights into the dynamic field of bioinformatics. Parallel Computing for Bioinformatics and Computational Biology is a contributed work that serves as a repository of case studies, collectively demonstrating how parallel computing streamlines difficult problems in bioinformatics and produces better results. Each of the chapters is authored by an established expert in the field and carefully edited to ensure a consistent approach and high standard throughout the publication. The work is organized into five parts: * Algorithms and models * Sequence analysis and microarrays * Phylogenetics * Protein folding * Platforms and enabling technologies Researchers, educators, and students in the field of bioinformatics will discover how high-performance computing can enable them to handle more complex data sets, gain deeper insights, and make new discoveries.

Reviews in Computational Chemistry, Volume 2

Author: Kenny B. Lipkowitz

Publisher: John Wiley & Sons

Published: 2009-09-22

Total Pages: 547

ISBN-13: 047012606X

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This second volume of the series 'Reviews in Computational Chemistry' explores new applications, new methodologies, and new perspectives. The topics covered include conformational analysis, protein folding, force field parameterizations, hydrogen bonding, charge distributions, electrostatic potentials, electronic spectroscopy, molecular property correlations, and the computational chemistry literature. Methodologies described include conformational search strategies, distance geometry, molecular mechanics, molecular dynamics, ab initio and semiempirical molecular orbital calculations, and quantitative structure-activity relationships (QSAR) using topological and electronic descriptors. A compendium of molecular modeling software will help users select the computational tools they need. Each chapter in 'Reviews in Computational Chemistry' serves as a brief tutorial for organic, physical, pharmaceutical, and biological chemists new to the field. Practitioners will be interested in the recent advances.