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Title Computational Biochemistry and Biophysics
Author Oren M. Becker
Publisher CRC Press
Release Date 2001-02-09
Category Science
Total Pages 512
ISBN 9780824741402
Language English, Spanish, and French
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Book Summary:

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 biomolecular properties gleaned from computer-generated membrane simulations. It also demonstrates comparative protein structure modeling, outlines computer-aided drug design, discusses Bayesian statistics in molecular and structural biology, and examines the RISM-SCF/MCSCF approach to chemical processes in solution.

Title An Introduction to Computational Biochemistry
Author C. Stan Tsai
Publisher John Wiley & Sons
Release Date 2003-03-31
Category Science
Total Pages 368
ISBN 9780471461098
Language English, Spanish, and French
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Book Summary:

This comprehensive text offers a solid introduction to the biochemical principles and skills required for any researcher applying computational tools to practical problems in biochemistry. Each chapter includes an introduction to the topic, a review of the biological concepts involved, a discussion of the programming and applications used, key references, and problem sets and answers. Providing detailed coverage of biochemical structures, enzyme reactions, metabolic simulation, genomic and proteomic analyses, and molecular modeling, this is the perfect resource for students and researchers in biochemistry, bioinformatics, bioengineering and computational science.

Title Computational Modeling of Biological Systems
Author Nikolay V Dokholyan
Publisher Springer Science & Business Media
Release Date 2012-02-10
Category Science
Total Pages 366
ISBN 9781461421467
Language English, Spanish, and French
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Book Summary:

Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.

Biomembrane Simulations by Max L. Berkowitz

Title Biomembrane Simulations
Author Max L. Berkowitz
Publisher CRC Press
Release Date 2019-04-30
Category Science
Total Pages 258
ISBN 9781351060301
Language English, Spanish, and French
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Book Summary:

Due to recent advancements in the development of numerical algorithms and computational hardware, computer simulations of biological membranes, often requiring use of substantial computational resources, are now reaching a mature stage. Since molecular processes in membranes occur on a multitude of spatial and time scales, molecular simulations of membranes can also serve as a testing ground for use of multi-scale simulation techniques. This book addresses some of the important issues related to understanding properties and behavior of model biological membranes and it Shows how simulations improve our understanding of biological membranes and makes connections with experimental results. Presents a careful discussion of the force fields used in the membrane simulations including detailed all-atom fields and coarse-grained fields. Presents a continuum description of membranes. Discusses a variety of issues such as influence of membrane surfaces on properties of water, interaction between membranes across water, nanoparticle permeation across the membrane, action of anesthetics and creation of inhomogeneous regions in membranes. Discusses important methodological issues when using simulations to examine phenomena such as pore creation and permeation across membranes. Discusses progress recently achieved in modeling bacterial membranes. It will be a valuable resource for graduate students, researchers and instructors in biochemistry, biophysics, pharmacology, physiology, and computational biology.

Title Entropy and Free Energy in Structural Biology
Author Hagai Meirovitch
Publisher CRC Press
Release Date 2020-08-14
Category Computers
Total Pages 374
ISBN 9781000072303
Language English, Spanish, and French
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Book Summary:

Computer simulation has become the main engine of development in statistical mechanics. In structural biology, computer simulation constitutes the main theoretical tool for structure determination of proteins and for calculation of the free energy of binding, which are important in drug design. Entropy and Free Energy in Structural Biology leads the reader to the simulation technology in a systematic way. The book, which is structured as a course, consists of four parts: Part I is a short course on probability theory emphasizing (1) the distinction between the notions of experimental probability, probability space, and the experimental probability on a computer, and (2) elaborating on the mathematical structure of product spaces. These concepts are essential for solving probability problems and devising simulation methods, in particular for calculating the entropy. Part II starts with a short review of classical thermodynamics from which a non-traditional derivation of statistical mechanics is devised. Theoretical aspects of statistical mechanics are reviewed extensively. Part III covers several topics in non-equilibrium thermodynamics and statistical mechanics close to equilibrium, such as Onsager relations, the two Fick's laws, and the Langevin and master equations. The Monte Carlo and molecular dynamics procedures are discussed as well. Part IV presents advanced simulation methods for polymers and protein systems, including techniques for conformational search and for calculating the potential of mean force and the chemical potential. Thermodynamic integration, methods for calculating the absolute entropy, and methodologies for calculating the absolute free energy of binding are evaluated. Enhanced by a number of solved problems and examples, this volume will be a valuable resource to advanced undergraduate and graduate students in chemistry, chemical engineering, biochemistry biophysics, pharmacology, and computational biology.

Title Theoretical Physics for Biological Systems
Author Paola Lecca
Publisher CRC Press
Release Date 2019-01-24
Category Medical
Total Pages 146
ISBN 9781351374316
Language English, Spanish, and French
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Book Summary:

Quantum physics provides the concepts and their mathematical formalization that lend themselves to describe important properties of biological networks topology, such as vulnerability to external stress and their dynamic response to changing physiological conditions. A theory of networks enhanced with mathematical concepts and tools of quantum physics opens a new area of biological physics, the one of systems biological physics.

Title The Physical Basis of Biochemistry
Author Peter R. Bergethon
Publisher Springer Science & Business Media
Release Date 2010-09-10
Category Science
Total Pages 949
ISBN 1441963243
Language English, Spanish, and French
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Book Summary:

Biological chemistry has changed since the completion of the human genome project. There is a renewed interest and market for individuals trained in biophysical chemistry and molecular biophysics. The Physical Basis of Biochemistry, Second Edition, emphasizes the interdisciplinary nature of biophysical chemistry by incorporating the quantitative perspective of the physical sciences without sacrificing the complexity and diversity of the biological systems, applies physical and chemical principles to the understanding of the biology of cells and explores the explosive developments in the area of genomics, and in turn, proteomics, bioinformatics, and computational and visualization technologies that have occurred in the past seven years. The book features problem sets and examples, clear illustrations, and extensive appendixes that provide additional information on related topics in mathematics, physics and chemistry.

Title Computational Molecular Modelling in Structural Biology
Author Anonim
Publisher Academic Press
Release Date 2018-08-24
Category Science
Total Pages 152
ISBN 9780128139172
Language English, Spanish, and French
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Book Summary:

Computational Molecular modelling in Structural Biology, Volume 113, the latest release in the Advances in Protein Chemistry and Structural Biology, highlights new advances in the field, with this new volume presenting interesting chapters on charting the Bromodomain BRD4: Towards the Identification of Novel Inhibitors with Molecular Similarity and Receptor Mapping, and Computational Methods to Discover Compounds for the Treatment of Chagas Disease. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Advances in Protein Chemistry and Structural Biology series Updated, with the latest information on Computational Molecular Modelling in Structural Biology

Biophysics by Mark C. Leake

Title Biophysics
Author Mark C. Leake
Publisher CRC Press
Release Date 2016-09-15
Category Medical
Total Pages 390
ISBN 9781498702461
Language English, Spanish, and French
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Book Summary:

An Up-to-Date Toolbox for Probing Biology Biophysics: Tools and Techniques covers the experimental and theoretical tools and techniques of biophysics. It addresses the purpose, science, and application of all physical science instrumentation and analysis methods used in current research labs. The book first presents the historical background, concepts, and motivation for using a physical science toolbox to understand biology. It then familiarizes students from the physical sciences with essential biological knowledge. The text subsequently focuses on experimental biophysical techniques that primarily detect biological components or measure/control biological forces. The author describes the science and application of key tools used in imaging, detection, general quantitation, and biomolecular interaction studies, which span multiple length and time scales of biological processes both in the test tube and in the living organism. Moving on to theoretical biophysics tools, the book presents computational and analytical mathematical methods for tackling challenging biological questions. It concludes with a discussion of the future of this exciting field. Future innovators will need to be trained in multidisciplinary science to be successful in industry, academia, and government support agencies. Addressing this challenge, this textbook educates future leaders on the development and application of novel physical science approaches to solve complex problems linked to biological questions.

Title Molecular Simulations and Biomembranes
Author Mark S. P. Sansom
Publisher Royal Society of Chemistry
Release Date 2010
Category Science
Total Pages 314
ISBN 9780854041893
Language English, Spanish, and French
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Book Summary:

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.

Cellular Biophysics And Modeling by Greg Conradi Smith

Title Cellular Biophysics and Modeling
Author Greg Conradi Smith
Publisher Cambridge University Press
Release Date 2019-03-31
Category Mathematics
Total Pages 396
ISBN 9781107005365
Language English, Spanish, and French
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Book Summary:

What every neuroscientist should know about the mathematical modeling of excitable cells, presented at an introductory level.

Title Computational Analysis of Biochemical Systems
Author Eberhard O. Voit
Publisher Cambridge University Press
Release Date 2000-09-04
Category Science
Total Pages 531
ISBN 0521785790
Language English, Spanish, and French
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Book Summary:

Teaches the use of modern computational methods for the analysis of biomedical systems using case studies and accompanying software.

Title Computational Approaches for Understanding Dynamical Systems Protein Folding and Assembly
Author Anonim
Publisher Academic Press
Release Date 2020-03-05
Category Science
Total Pages 552
ISBN 9780128211373
Language English, Spanish, and French
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Book Summary:

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

Computational Biology by Ralf Blossey

Title Computational Biology
Author Ralf Blossey
Publisher CRC Press
Release Date 2019-06-11
Category Computers
Total Pages 285
ISBN 9780429994616
Language English, Spanish, and French
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Book Summary:

Computational biology has developed rapidly during the last two decades following the genomic revolution which culminated in the sequencing of the human genome. More than ever it has developed into a field which embraces computational methods from different branches of the exact sciences: pure and applied mathematics, computer science, theoretical physics. This Second Edition provides a solid introduction to the techniques of statistical mechanics for graduate students and researchers in computational biology and biophysics. Material has been reorganized to clarify equilbrium and nonequilibrium aspects of biomolecular systems Content has been expanded, in particular in the treatment of the electrostatic interactions of biomolecules and the application of non-equilibrium statistical mechanics to biomolecules New network-based approaches for the study of proteins are presented. All treated topics are put firmly in the context of the current research literature, allowing the reader to easily follow an individual path into a specific research field. Exercises and Tasks accompany the presentations of the topics with the intention of enabling the readers to test their comprehension of the developed basic concepts.

Title Dynamics of Proteins and Nucleic Acids
Author J. Andrew McCammon
Publisher Cambridge University Press
Release Date 1988-04-29
Category Science
Total Pages 248
ISBN 0521356520
Language English, Spanish, and French
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Book Summary:

This book is a self-contained introduction to the theory of atomic motion in proteins and nucleic acids. An understanding of such motion is essential because it plays a crucially important role in biological activity. The authors, both of whom are well known for their work in this field, describe in detail the major theoretical methods that are likely to be useful in the computer-aided design of drugs, enzymes and other molecules. A variety of theoretical and experimental studies is described and these are critically analyzed to provide a comprehensive picture of dynamic aspects of biomolecular structure and function. The book will be of interest to graduate students and research workers in structural biochemistry (X-ray diffraction and NMR), theoretical chemistry (liquids and polymers), biophysics, enzymology, molecular biology, pharmaceutical chemistry, genetic engineering and biotechnology.

Biophysics Of Dna by Alexander Vologodskii

Title Biophysics of DNA
Author Alexander Vologodskii
Publisher Cambridge University Press
Release Date 2015-03-12
Category Science
Total Pages 272
ISBN 9781107034938
Language English, Spanish, and French
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Book Summary:

Surveys the last sixty years of research in the rapidly advancing field of DNA biophysics, addressing key questions and facilitating further research.

Title Computational Approaches to Protein Dynamics
Author Monika Fuxreiter
Publisher CRC Press
Release Date 2014-12-24
Category Science
Total Pages 479
ISBN 9781482297867
Language English, Spanish, and French
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Book Summary:

The Latest Developments on the Role of Dynamics in Protein Functions Computational 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, and biology show how these advanced methods provide insights into dynamic aspects of biochemical processes. A particular focus is on intrinsically disordered proteins (IDPs), which lack a well-defined three-dimensional structure and function as dynamic ensembles. The book covers a wide spectrum of dynamics, from electronic structure-based to coarse-grained techniques via multiscaling at different levels. After an introduction to dynamics and historical overview of basic methodologies, the book addresses the following issues: Is there a quantitative relationship between enzymatic catalysis and protein dynamics? Which are the functionally relevant motions of proteins? How can structural properties and partner recognition mechanisms of IDPs be simulated? How can we speed up molecular dynamics? How can we describe conformational ensembles by the synergistic effort of computations and experiments? While dynamics is now considered essential for interpreting protein action, it is not yet an integral component in establishing structure–function relationships of proteins. Helping to reshape this classical view in biochemistry, this groundbreaking book explores advances in computational methodology and contributes to the new, ensemble way of studying proteins.

Title Computational and Visualization Techniques for Structural Bioinformatics Using Chimera
Author Forbes J. Burkowski
Publisher CRC Press
Release Date 2014-07-29
Category Science
Total Pages 461
ISBN 9781439836620
Language English, Spanish, and French
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Book Summary:

A Step-by-Step Guide to Describing Biomolecular Structure Computational and Visualization Techniques for Structural Bioinformatics Using Chimera shows how to perform computations with Python scripts in the Chimera environment. It focuses on the three core areas needed to study structural bioinformatics: biochemistry, mathematics, and computation. Understand Important Concepts of Structural Bioinformatics The book covers topics that deal primarily with protein structure and includes many exercises that are grounded in biological problems at the molecular level. The text encourages mathematical analysis by providing a firm foundation for computations. It analyzes numerous Python scripts for the Chimera environment, with the scripts and other material available on a supplementary website. Build Python Scripts to Extend the Capabilities of Chimera Through more than 60 exercises that involve the development of Python scripts, the book gives you concrete guidance on using the scripting capabilities of Chimera. You’ll gain experience in solving real problems as well as understand the various applications of linear algebra. You can also use the scripts as starting points for the development of similar applications and use classes from the StructBio toolkit for computations, such as structure overlap, data plotting, scenographics, and display of residue networks.

Title Frontiers in Computational Chemistry Volume 1
Author Zaheer Ul-Haq
Publisher Elsevier
Release Date 2015-12-14
Category Science
Total Pages 362
ISBN 9781608058648
Language English, Spanish, and French
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Book Summary:

Frontiers in Computational Chemistry, originally published by Bentham and now distributed by Elsevier, presents the latest research findings and methods in the diverse field of computational chemistry, focusing on molecular modeling techniques used in drug discovery and the drug development process. This includes computer-aided molecular design, drug discovery and development, lead generation, lead optimization, database management, computer and molecular graphics, and the development of new computational methods or efficient algorithms for the simulation of chemical phenomena including analyses of biological activity. In Volume 1, the leading researchers in the field have collected eight different perspectives in the application of computational methods towards drug design to provide an up-to-date rendering of the current field. This volume covers a variety of topics from G protein-coupled receptors, to the use of cheminformatics and bioinformatics, computational tools such as Molecular Mechanics Poisson-Boltzmann Surface Area, protein-protein interactions, the use of computational methods on large biological data sets, various computational methods used to identify pharmaceutically relevant targets, and more. Brings together a wide range of research into a single collection to help researchers keep up with new methods Uniquely focuses on computational chemistry approaches that can accelerate drug design Makes a solid connection between experiment and computation and the novel application of computational methods in the fields of biology, chemistry, biochemistry, physics, and biophysics, with particular focus on the integration of computational methods with experimental data

Title Computational Systems Biology
Author Andres Kriete
Publisher Academic Press
Release Date 2013-11-26
Category Computers
Total Pages 548
ISBN 9780124059382
Language English, Spanish, and French
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Book Summary:

This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. Logical information flow aids understanding of basic building blocks of life through disease phenotypes Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.