Guide to Biomolecular Simulations

Guide to Biomolecular Simulations
Author: Oren M. Becker
Publisher: Springer Science & Business Media
Total Pages: 225
Release: 2006-06-26
Genre: Science
ISBN: 140203587X

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Molecular dynamics simulations have become instrumental in replacing our view of proteins as relatively rigid structures with the realization that they were dynamic systems, whose internal motions play a functional role. Over the years, such simulations have become a central part of biophysics. Applications of molecular dynamics in biophysics range over many areas. They are used in the structure determination of macromolecules with x-ray and NMR data, the modelling of unknown structures from their sequence, the study of enzyme mechanisms, the estimation of ligand-binding free energies, the evaluation of the role of conformational change in protein function, and drug design for targets of known structures. The widespread application of molecular dynamics and related methodologies suggests that it would be useful to have available an introductory self-contained course by which students with a relatively limited background in chemistry, biology and computer literacy, can learn the fundamentals of the field. This Guide to Biomolecular Simulations tries to fill this need. The Guide consists of six chapters which provide the fundamentals of the field and six chapters which introduce the reader to more specialized but important applications of the methodology.

Molecular Modeling and Simulation

Molecular Modeling and Simulation
Author: Tamar Schlick
Publisher: Springer Science & Business Media
Total Pages: 669
Release: 2013-04-18
Genre: Science
ISBN: 0387224645

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Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text

Biomolecular Simulations in Structure-Based Drug Discovery

Biomolecular Simulations in Structure-Based Drug Discovery
Author: Francesco L. Gervasio
Publisher: John Wiley & Sons
Total Pages: 368
Release: 2019-04-29
Genre: Medical
ISBN: 3527342656

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A guide to applying the power of modern simulation tools to better drug design Biomolecular Simulations in Structure-based Drug Discovery offers an up-to-date and comprehensive review of modern simulation tools and their applications in real-life drug discovery, for better and quicker results in structure-based drug design. The authors describe common tools used in the biomolecular simulation of drugs and their targets and offer an analysis of the accuracy of the predictions. They also show how to integrate modeling with other experimental data. Filled with numerous case studies from different therapeutic fields, the book helps professionals to quickly adopt these new methods for their current projects. Experts from the pharmaceutical industry and academic institutions present real-life examples for important target classes such as GPCRs, ion channels and amyloids as well as for common challenges in structure-based drug discovery. Biomolecular Simulations in Structure-based Drug Discovery is an important resource that: -Contains a review of the current generation of biomolecular simulation tools that have the robustness and speed that allows them to be used as routine tools by non-specialists -Includes information on the novel methods and strategies for the modeling of drug-target interactions within the framework of real-life drug discovery and development -Offers numerous illustrative case studies from a wide-range of therapeutic fields -Presents an application-oriented reference that is ideal for those working in the various fields Written for medicinal chemists, professionals in the pharmaceutical industry, and pharmaceutical chemists, Biomolecular Simulations in Structure-based Drug Discovery is a comprehensive resource to modern simulation tools that complement and have the potential to complement or replace laboratory assays for better results in drug design.

Biomolecular Simulation

Biomolecular Simulation
Author: Wilfred F. van Gunsteren
Publisher:
Total Pages: 757
Release: 1996
Genre: Biomoleculen / gtt
ISBN: 9783728124227

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Computer Applications -- Physical Sciences and Engineering.

Biomolecular Simulations

Biomolecular Simulations
Author: Massimiliano Bonomi
Publisher: Humana
Total Pages: 581
Release: 2020-08-14
Genre: Science
ISBN: 9781493996100

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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.

A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules
Author: Yong Wang
Publisher:
Total Pages: 0
Release: 2023
Genre: SCIENCE
ISBN: 9780735425255

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Biomolecular modeling and simulation are becoming increasingly crucial for understanding the microscopic biological world with high time and spatial recognition. A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules offers guidance for advanced multiscale modeling and machine learning-aided molecular simulations. The book provides reproducible, step-by-step instructions on the scripts and codes needed to complete the simulations. It offers readers tips, tricks, and troubleshooting advice for the reader's real-life challenges. Topics in this book focus on the latest developments and: Provide an overview of current methods and techniques; Serve as a tutorial and an in-depth historical record of the topic; Contain step-by-step instructions for the methods used in molecular modeling and simulation of biomolecules. A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules is a key resource for students and researchers in biology, biophysics, biochemistry, and computational chemistry.

Biomolecular Simulations

Biomolecular Simulations
Author: Massimiliano Bonomi
Publisher:
Total Pages: 581
Release: 2019
Genre: Biochemistry
ISBN: 9781493996087

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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.

A Practical Introduction to the Simulation of Molecular Systems

A Practical Introduction to the Simulation of Molecular Systems
Author: Martin J. Field
Publisher: Cambridge University Press
Total Pages: 294
Release: 2007-07-19
Genre: Science
ISBN: 1139465813

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Molecular simulation is a powerful tool in materials science, physics, chemistry and biomolecular fields. This updated edition provides a pragmatic introduction to a wide range of techniques for the simulation of molecular systems at the atomic level. The first part concentrates on methods for calculating the potential energy of a molecular system, with new chapters on quantum chemical, molecular mechanical and hybrid potential techniques. The second part describes methods examining conformational, dynamical and thermodynamical properties of systems, covering techniques including geometry-optimization, normal-mode analysis, molecular dynamics, and Monte Carlo simulation. Using Python, the second edition includes numerous examples and program modules for each simulation technique, allowing the reader to perform the calculations and appreciate the inherent difficulties involved in each. This is a valuable resource for researchers and graduate students wanting to know how to use atomic-scale molecular simulations. Supplementary material, including the program library and technical information, available through www.cambridge.org/9780521852524.

Biomolecular and Bioanalytical Techniques

Biomolecular and Bioanalytical Techniques
Author: Vasudevan Ramesh
Publisher: John Wiley & Sons
Total Pages: 576
Release: 2019-06-10
Genre: Science
ISBN: 1119483964

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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.

Computational Modeling And Simulations Of Biomolecular Systems

Computational Modeling And Simulations Of Biomolecular Systems
Author: Benoit Roux
Publisher: World Scientific
Total Pages: 209
Release: 2021-08-23
Genre: Computers
ISBN: 9811232776

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This textbook originated from the course 'Simulation, Modeling, and Computations in Biophysics' that I have taught at the University of Chicago since 2011. The students typically came from a wide range of backgrounds, including biology, physics, chemistry, biochemistry, and mathematics, and the course was intentionally adapted for senior undergraduate students and graduate students. This is not a highly technical book dedicated to specialists. The objective is to provide a broad survey from the physical description of a complex molecular system at the most fundamental level, to the type of phenomenological models commonly used to represent the function of large biological macromolecular machines.The key conceptual elements serving as building blocks in the formulation of different levels of approximations are introduced along the way, aiming to clarify as much as possible how they are interrelated. The only assumption is a basic familiarity with simple mathematics (calculus and integrals, ordinary differential equations, matrix linear algebra, and Fourier-Laplace transforms).