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Author: David A. Case
Publisher: University of California, San Francisco
ISBN:
Category : Computers
Languages : en
Pages : 1016
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Book Description
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations.[1, 2] The term Amber is also used to refer to the empirical force fields that are implemented here.[3, 4] It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools23, a collection of freely available programs mostly under the GPL license, and Amber22, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber22 represents a significant change from the most recent previous version, Amber20. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.
Author: David A. Case
Publisher: University of California, San Francisco
ISBN:
Category : Computers
Languages : en
Pages : 1016
Get Book Here
Book Description
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations.[1, 2] The term Amber is also used to refer to the empirical force fields that are implemented here.[3, 4] It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools23, a collection of freely available programs mostly under the GPL license, and Amber22, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber22 represents a significant change from the most recent previous version, Amber20. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.
Author: David A. Case
Publisher: University of California, San Francisco
ISBN:
Category : Computers
Languages : en
Pages : 998
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Book Description
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term Amber is also used to refer to the empirical force fields that are implemented here. It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools22, a collection of freely available programs mostly under the GPL license, and Amber22, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber22 represents a significant change from the most recent previous version, Amber20. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.
Author: Teresa Carlomagno
Publisher: Springer Nature
ISBN: 1071633937
Category : Science
Languages : en
Pages : 375
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Book Description
This volume looks at the latest methods used to study and modulate the biological function and mechanisms of SH2 domains. The chapters in this book are organized into five parts. Part One presents methodology aimed at determining the structures and dynamics of SH2 domains and their complexes with phosphopeptides. Part Two discusses techniques to understand and predict interactions of SH2 domains by measuring or calculating their affinity to phosphopeptides. Part Three focuses on inhibitors of SH2 domains that lead the way for chemical tool development and drug discovery. Part Four describes how to evolve and engineer SH2 domains with specific binding properties, and Part Five explores how to measure the regulation of protein tyrosine phosphatase activity through allosteric binding of peptides to SH2 domains and condensation. 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, SH2 Domains: Functional Modules and Evolving Tools in Biology is a valuable resource for researchers, working in the biophysical and biochemical field, who want to learn more about this exciting and versatile class of regulatory and signaling domains.
Author: K. Dane Wittrup
Publisher: MIT Press
ISBN: 0262042657
Category : Science
Languages : en
Pages : 593
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Book Description
A comprehensive presentation of essential topics for biological engineers, focusing on the development and application of dynamic models of biomolecular and cellular phenomena. This book describes the fundamental molecular and cellular events responsible for biological function, develops models to study biomolecular and cellular phenomena, and shows, with examples, how models are applied in the design and interpretation of experiments on biological systems. Integrating molecular cell biology with quantitative engineering analysis and design, it is the first textbook to offer a comprehensive presentation of these essential topics for chemical and biological engineering. The book systematically develops the concepts necessary to understand and study complex biological phenomena, moving from the simplest elements at the smallest scale and progressively adding complexity at the cellular organizational level, focusing on experimental testing of mechanistic hypotheses. After introducing the motivations for formulation of mathematical rate process models in biology, the text goes on to cover such topics as noncovalent binding interactions; quantitative descriptions of the transient, steady state, and equilibrium interactions of proteins and their ligands; enzyme kinetics; gene expression and protein trafficking; network dynamics; quantitative descriptions of growth dynamics; coupled transport and reaction; and discrete stochastic processes. The textbook is intended for advanced undergraduate and graduate courses in chemical engineering and bioengineering, and has been developed by the authors for classes they teach at MIT and the University of Minnesota.
Author: Alberto Podjarny
Publisher: Royal Society of Chemistry
ISBN: 1849732663
Category : Science
Languages : en
Pages : 373
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Book Description
The binding of small ligands to biological molecules is central to most aspects of biological function. The past twenty years has seen the development of an increasing armoury of biophysical methods that not only detect such binding, but also provide varying degrees of information about the kinetics, thermodynamics and structural aspects of the process. These methods have received increasing attention with the growth in more rational approaches to drug discovery and design. This book reviews the latest advances in the application of biophysics to the study of ligand binding. It provides a complete overview of current techniques to identify ligands, characterise their binding sites and understand their binding mechanisms. Particular emphasis is given to the combined use of different techniques and their relative strengths and weaknesses. Consistency in the way each technique is described makes it easy for readers to select the most suitable protocol for their research. The introduction explains why some techniques are more suitable than others and emphasizes the possible synergies between them. The following chapters, all written by a specialist in the particular technique, focus on each method individually. The book finishes by describing how several complimentary techniques can be used together for maximum effectiveness. This book is suitable for biomolecular scientists at graduate or post-doctoral level in academia and industry. Biologists and chemists will also find it a useful introduction to the techniques available.
Author: Domitilla Del Vecchio
Publisher: Princeton University Press
ISBN: 1400850509
Category : Science
Languages : en
Pages : 287
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Book Description
This book provides an accessible introduction to the principles and tools for modeling, analyzing, and synthesizing biomolecular systems. It begins with modeling tools such as reaction-rate equations, reduced-order models, stochastic models, and specific models of important core processes. It then describes in detail the control and dynamical systems tools used to analyze these models. These include tools for analyzing stability of equilibria, limit cycles, robustness, and parameter uncertainty. Modeling and analysis techniques are then applied to design examples from both natural systems and synthetic biomolecular circuits. In addition, this comprehensive book addresses the problem of modular composition of synthetic circuits, the tools for analyzing the extent of modularity, and the design techniques for ensuring modular behavior. It also looks at design trade-offs, focusing on perturbations due to noise and competition for shared cellular resources. Featuring numerous exercises and illustrations throughout, Biomolecular Feedback Systems is the ideal textbook for advanced undergraduates and graduate students. For researchers, it can also serve as a self-contained reference on the feedback control techniques that can be applied to biomolecular systems. Provides a user-friendly introduction to essential concepts, tools, and applications Covers the most commonly used modeling methods Addresses the modular design problem for biomolecular systems Uses design examples from both natural systems and synthetic circuits Solutions manual (available only to professors at press.princeton.edu) An online illustration package is available to professors at press.princeton.edu
Author: Hiroshi Wada
Publisher: World Scientific
ISBN: 9812770178
Category : Medical
Languages : en
Pages : 182
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Book Description
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Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 1436
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Book Description
Author: Vasudevan Ramesh
Publisher: John Wiley & Sons
ISBN: 1119483964
Category : Science
Languages : en
Pages : 576
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Book Description
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.
Author:
Publisher:
ISBN:
Category : Aeronautics
Languages : en
Pages : 716
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Book Description
