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Modeling Biomolecular Site Dynamics, William S. Hlavacek


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Автор: William S. Hlavacek
Название:  Modeling Biomolecular Site Dynamics
ISBN: 9781493991006
Издательство: Springer
Классификация:



ISBN-10: 1493991000
Обложка/Формат: Hardcover
Страницы: 423
Вес: 1.05 кг.
Дата издания: 2019
Серия: Methods in Molecular Biology
Язык: English
Издание: 1st ed. 2019
Иллюстрации: 105 tables, color; 108 illustrations, color; 80 illustrations, black and white; xix, 423 p. 188 illus., 108 illus. in color. with online files/update.
Размер: 254 x 178 x 25
Читательская аудитория: Professional & vocational
Основная тема: Life Sciences
Подзаголовок: Methods and Protocols
Ссылка на Издательство: Link
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Поставляется из: Германии
Описание:
This volume covers a variety of topics related to the practice of rule-based modeling, a type of mathematical modeling useful for studying biomolecular site dynamics. There is an emphasis on software tools and detailed descriptions of techniques. The chapters in this book discuss topics such as software tools and frameworks for compartmental modeling (Pycellerator, RuleBuilder, Prgy, rxncon, MSMB, and ML-Rules); tools for spatial modeling (Simmune, Smoldyn, MCell-R, SRSim, and CellOrganizer); rule-based models to analyze proteomic data; model annotation; Markov chain aggregation; BioJazz; and methods to identify model parameters (Data2Dynamics, RKappa, and BioNetFit). Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary resources, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.
Cutting-edge and thorough, Modeling Biomolecular Site Dynamics: Methods and Protocols is a valuable resource for both the novice and expert rule-based modeler. It will also appeal to systems biologists and help them enhance their studies with easy-to-read and write rule-based models.

Дополнительное описание:
A Pycellerator Tutorial.- Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules.- Strategy-Driven Exploration for Rule-Based Models of Biochemical Systems with PORGY.- Using rxncon to Develop Rule-Based



Modeling Biomolecular Networks in Cells

Автор: Luonan Chen; Ruiqi Wang; Chunguang Li; Kazuyuki Ai
Название: Modeling Biomolecular Networks in Cells
ISBN: 1447157362 ISBN-13(EAN): 9781447157366
Издательство: Springer
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Цена: 18284.00 р.
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Описание: Modeling Biomolecular Networks in Cells shows how the interaction between the molecular components of basic living organisms can be modelled mathematically and the models used to create artificial biological entities within cells.

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechani

Автор: Liwo Adam
Название: Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechani
ISBN: 3319958429 ISBN-13(EAN): 9783319958422
Издательство: Springer
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Цена: 34937.00 р.
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Описание: This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.

Physics at the Biomolecular Interface

Автор: Fern?ndez
Название: Physics at the Biomolecular Interface
ISBN: 3319308513 ISBN-13(EAN): 9783319308517
Издательство: Springer
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Цена: 20896.00 р.
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Описание: This bookfocuses primarily on the role of interfacial forces in understanding biologicalphenomena at the molecular scale. By providing a suitable statisticalmechanical apparatus to handle the biomolecular interface, the book becomesuniquely positioned to address core problems in molecular biophysics. Ithighlights the importance of interfacial tension in delineating a solution tothe protein folding problem, in unravelling the physico-chemical basis ofenzyme catalysis and protein associations, and in rationally designingmolecular targeted therapies. Thus grounded in fundamental science, the bookdevelops a powerful technological platform for drug discovery, while it is setto inspire scientists at any level in their careers determined to address themajor challenges in molecular biophysics.Theacknowledgment of how exquisitely the structure and dynamics of proteins and theiraqueous environment are related attests to the overdue recognition thatbiomolecular phenomena cannot be effectively understood without dealing withinterfacial behaviour. There is an urge to grasp how biologically relevantbehaviour is shaped by the structuring of biomolecular interfaces and howinterfacial tension affects the molecular events that take place in the cell.This book squarely addresses these needs from a physicist perspective.Thebook may serve as a monograph for practitioners and, alternatively, as anadvanced textbook. Fruitful reading requires a background in physical chemistryand some basics in biophysics. The selected problems at the end of the chaptersand the progression in conceptual difficulty make it a suitable textbook for agraduate level course or an elective course for seniors majoring in chemistry,physics, biomedical engineering or related disciplines.

Biomolecular Simulations

Автор: Luca Monticelli; Emppu Salonen
Название: Biomolecular Simulations
ISBN: 1493958917 ISBN-13(EAN): 9781493958917
Издательство: Springer
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Цена: 27950.00 р.
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Описание: 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

Автор: Massimiliano Bonomi; Carlo Camilloni
Название: Biomolecular Simulations
ISBN: 149399607X ISBN-13(EAN): 9781493996070
Издательство: Springer
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Цена: 25155.00 р.
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Описание:

This volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; Part Two discusses enhanced sampling and free-energy calculations; Part Three talks about integrative computational and experimental approaches for biomolecular simulations; and Part Four focuses on analyzing, visualizing, and comparing biomolecular simulations. 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, Biomolecular Simulations: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in studying different areas of biomolecular simulations, and discovering new tools to progress their future projects.
Properties and Chemistry of Biomolecular Systems

Автор: N. Russo; Jane Anastassopoulou; Guido Barone
Название: Properties and Chemistry of Biomolecular Systems
ISBN: 9401043531 ISBN-13(EAN): 9789401043533
Издательство: Springer
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Цена: 22203.00 р.
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Описание: Proceedings of the Second Joint Greek--Italian Meeting on Chemistry and Biological Systems and Molecular Chemical Engineering, Cetraro, Italy, October 1992


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