Biomolecular Simulations Methods And Protocols
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Biomolecular Simulations
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Author : Luca Monticelli
language : en
Publisher: Humana Press
Release Date : 2012-10-04
Biomolecular Simulations written by Luca Monticelli and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-10-04 with Science categories.
Over the past 40 years the field of molecular simulations has evolved from picosecond studies of isolated macromolecules in vacuum to studies of complex, chemically heterogeneous biological systems consisting of millions of atoms, with the simulation time scales spanning up to milliseconds. In Biomolecular Simulations: Methods and Protocols, expert researchers illustrate many of the methods commonly used in molecular modelling of biological systems, including methods for electronic structure calculations, classical molecular dynamics simulations and coarse-grained techniques. A selection of advanced techniques and recent methodological developments, which rarely find coverage in traditional textbooks, is also introduced. Written in the highly successful Methods in Molecular Biology series format, chapters include general introductions to well-established computational methodologies, applications to real-world biological systems, as well as practical tips and general protocols on carrying out biomolecular simulations. Special emphasis is placed on simulations of proteins, lipids, nucleic acids, and carbohydrates. Authoritative and practical, Biomolecular Simulations: Methods and Protocols seeks to aid scientists in further simulation studies of biological systems.
Biomolecular Simulations Methods And Protocols
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Author : Mr. Rohit Manglik
language : en
Publisher: EduGorilla Publication
Release Date : 2024-07-18
Biomolecular Simulations Methods And Protocols written by Mr. Rohit Manglik and has been published by EduGorilla Publication this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-07-18 with Science categories.
EduGorilla Publication is a trusted name in the education sector, committed to empowering learners with high-quality study materials and resources. Specializing in competitive exams and academic support, EduGorilla provides comprehensive and well-structured content tailored to meet the needs of students across various streams and levels.
Molecular Modeling Of Proteins
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Author : Andreas Kukol
language : en
Publisher: Humana Press
Release Date : 2017-04-30
Molecular Modeling Of Proteins written by Andreas Kukol and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-04-30 with Science categories.
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.
Hidden Markov Models
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Author : David R. Westhead
language : en
Publisher: Humana
Release Date : 2017-02-22
Hidden Markov Models written by David R. Westhead and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-02-22 with Science categories.
This volume aims to provide a new perspective on the broader usage of Hidden Markov Models (HMMs) in biology. Hidden Markov Models: Methods and Protocols guides readers through chapters on biological systems; ranging from single biomolecule, cellular level, and to organism level and the use of HMMs in unravelling the complex mechanisms that govern these complex systems. 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 practical, Hidden Markov Models: Methods and Protocols aims to demonstrate the impact of HMM in biology and inspire new research.
Computational Methods To Study The Structure And Dynamics Of Biomolecules And Biomolecular Processes
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Author : Adam Liwo
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-07-17
Computational Methods To Study The Structure And Dynamics Of Biomolecules And Biomolecular Processes written by Adam Liwo and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-07-17 with Technology & Engineering categories.
Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.
Protein Folding
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Author : Victor Muñoz
language : en
Publisher: Humana
Release Date : 2021-11-30
Protein Folding written by Victor Muñoz and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-11-30 with Science categories.
This volume provides comprehensive protocols on experimental and computational methods that are used to study probe protein folding reactions and mechanisms. Chapters divided into five parts detail protein engineering, protein chemistry, experimental approaches to investigate the thermodynamics and kinetics of protein folding transitions, probe protein folding at the single molecule, analysis and interpretation of computer simulations, procedures and tools for the prediction of protein folding properties. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Protein Folding: Methods and Protocols aims to be a useful practical guide to researches to help further their study in this field.
Combined Quantum Mechanical And Molecular Mechanical Modelling Of Biomolecular Interactions
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Author :
language : en
Publisher: Academic Press
Release Date : 2015-11-16
Combined Quantum Mechanical And Molecular Mechanical Modelling Of Biomolecular Interactions written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-11-16 with Science categories.
Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions continues the tradition of the Advances in Protein Chemistry and Structural Biology series has been the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins, with each thematically organized volume guest edited by leading experts in a broad range of protein-related topics. - Describes advances in application of powerful techniques in the biosciences - Provides cutting-edge developments in protein chemistry and structural biology - Chapters are written by authorities in their field - Targeted to a wide audience of researchers, specialists, and students
Understanding Molecular Simulation
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Author : Daan Frenkel
language : en
Publisher: Elsevier
Release Date : 2023-07-13
Understanding Molecular Simulation written by Daan Frenkel and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-07-13 with Science categories.
Understanding Molecular Simulation explains molecular simulation from a chemical-physics and statistical-mechanics perspective. It highlights how physical concepts are used to develop better algorithms and expand the range of applicability of simulations. Understanding Molecular Simulation is equally relevant for those who develop new code and those who use existing packages. Both groups are continuously confronted with the question of which computational technique best suits a given application. Understanding Molecular Simulation provides readers with the foundational knowledge they need to learn about, select and apply the most appropriate of these tools to their own work. The implementation of simulation methods is illustrated in pseudocodes, and their practical use is shown via case studies presented throughout the text. Since the second edition's publication, the simulation world has expanded significantly: existing techniques have continued to develop, and new ones have emerged, opening up novel application areas. This new edition aims to describe these new developments without becoming exhaustive; examples are included that highlight current uses, and several new examples have been added to illustrate recent applications. Examples, case studies, questions, and downloadable algorithms are also included to support learning. No prior knowledge of computer simulation is assumed. - Fully updated guide to both the current state and latest developments in the field of molecular simulation, including added and expanded information on such topics as molecular dynamics and statistical assessment of simulation results - Gives a rounded overview by showing fundamental background information in practice via new examples in a range of key fields - Provides online access to new data, algorithms and tutorial slides to support and encourage practice and learning
Computer Aided Antibody Design
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Author : Kouhei Tsumoto
language : en
Publisher: Springer Nature
Release Date : 2022-11-08
Computer Aided Antibody Design written by Kouhei Tsumoto and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-11-08 with Medical categories.
This volume details state-of-the- art methods on computer-aided antibody design. Chapters guide readers through information on antibody sequences and structures, modeling antibody structures and dynamics, prediction and optimization of biological and biophysical properties of antibodies, prediction of antibody-antigen interactions, and computer-aided antibody affinity maturation and beyond. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Computer-Aided Antibody Design aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge. Chapter 2 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Computer Simulation Of Liquids
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Author : M. P. Allen
language : en
Publisher: Oxford University Press
Release Date : 2017
Computer Simulation Of Liquids written by M. P. Allen and has been published by Oxford University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with Computers categories.
This is the second edition of a widely used practical guide to computer simulations of liquids. The technique uses a model for the way molecules interact, to predict how large numbers of them behave in liquid state. This essential introduction to this rapidly growing field is complete with illustrative computer code.