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Protein Simulations
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Book Synopsis Protein Simulations by : Valerie Daggett
Download or read book Protein Simulations written by Valerie Daggett and published by Elsevier. This book was released on 2003-11-26 with total page 477 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function.* Force Fields* Ligand Binding* Protein Membrane Simulation* Enzyme Dynamics* Protein Folding and unfolding simulations
Book Synopsis Computer Simulations of Aggregation of Proteins and Peptides by : Mai Suan Li
Download or read book Computer Simulations of Aggregation of Proteins and Peptides written by Mai Suan Li and published by Humana. This book was released on 2022-02-16 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides computational methods and reviews various aspects of computational studies of protein aggregation. Chapters discuss the relationship between protein misfolding and protein aggregation, methods of prediction of aggregation propensities of protein, peptides, protein structure, results of computer simulations of aggregation, and computational simulations focused on specific diseases such as Alzheimer’s, Parkinson’s, and preeclampsia. 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 cutting-edge, Computer Simulations of Aggregation of Proteins and Peptides aims to ensure successful results in the further study of this vital field.
Book Synopsis Molecular Modeling of Proteins by : Andreas Kukol
Download or read book Molecular Modeling of Proteins written by Andreas Kukol and published by Humana Press. This book was released on 2017-04-30 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly by :
Download or read book Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly written by and published by Academic Press. This book was released on 2020-03-05 with total page 554 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Book Synopsis Computer Simulations of Protein Structures and Interactions by : Serafin Fraga
Download or read book Computer Simulations of Protein Structures and Interactions written by Serafin Fraga and published by Springer Science & Business Media. This book was released on 2013-04-17 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.
Book Synopsis Molecular Simulations by : Saman Alavi
Download or read book Molecular Simulations written by Saman Alavi and published by John Wiley & Sons. This book was released on 2020-06-29 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides hands-on knowledge enabling students of and researchers in chemistry, biology, and engineering to perform molecular simulations This book introduces the fundamentals of molecular simulations for a broad, practice-oriented audience and presents a thorough overview of the underlying concepts. It covers classical mechanics for many-molecule systems as well as force-field models in classical molecular dynamics; introduces probability concepts and statistical mechanics; and analyzes numerous simulation methods, techniques, and applications. Molecular Simulations: Fundamentals and Practice starts by covering Newton's equations, which form the basis of classical mechanics, then continues on to force-field methods for modelling potential energy surfaces. It gives an account of probability concepts before subsequently introducing readers to statistical and quantum mechanics. In addition to Monte-Carlo methods, which are based on random sampling, the core of the book covers molecular dynamics simulations in detail and shows how to derive critical physical parameters. It finishes by presenting advanced techniques, and gives invaluable advice on how to set up simulations for a diverse range of applications. -Addresses the current need of students of and researchers in chemistry, biology, and engineering to understand and perform their own molecular simulations -Covers the nitty-gritty ? from Newton's equations and classical mechanics over force-field methods, potential energy surfaces, and probability concepts to statistical and quantum mechanics -Introduces physical, chemical, and mathematical background knowledge in direct relation with simulation practice -Highlights deterministic approaches and random sampling (eg: molecular dynamics versus Monte-Carlo methods) -Contains advanced techniques and practical advice for setting up different simulations to prepare readers entering this exciting field Molecular Simulations: Fundamentals and Practice is an excellent book benefitting chemist, biologists, engineers as well as materials scientists and those involved in biotechnology.
Book Synopsis Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations by : Valentina Tozzini
Download or read book Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations written by Valentina Tozzini and published by Frontiers Media SA. This book was released on 2020-10-27 with total page 235 pages. Available in PDF, EPUB and Kindle. Book excerpt: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Book Synopsis Scientific Modeling and Simulations by : Sidney Yip
Download or read book Scientific Modeling and Simulations written by Sidney Yip and published by Springer Science & Business Media. This book was released on 2010-04-07 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although computational modeling and simulation of material deformation was initiated with the study of structurally simple materials and inert environments, there is an increasing demand for predictive simulation of more realistic material structure and physical conditions. In particular, it is recognized that applied mechanical force can plausibly alter chemical reactions inside materials or at material interfaces, though the fundamental reasons for this chemomechanical coupling are studied in a material-speci c manner. Atomistic-level s- ulations can provide insight into the unit processes that facilitate kinetic reactions within complex materials, but the typical nanosecond timescales of such simulations are in contrast to the second-scale to hour-scale timescales of experimentally accessible or technologically relevant timescales. Further, in complex materials these key unit processes are “rare events” due to the high energy barriers associated with those processes. Examples of such rare events include unbinding between two proteins that tether biological cells to extracellular materials [1], unfolding of complex polymers, stiffness and bond breaking in amorphous glass bers and gels [2], and diffusive hops of point defects within crystalline alloys [3].
Book Synopsis Biomolecular Simulations by : Massimiliano Bonomi
Download or read book Biomolecular Simulations written by Massimiliano Bonomi and published by Humana. This book was released on 2019-08-08 with total page 581 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Molecular Simulations and Biomembranes by : Mark S P Sansom
Download or read book Molecular Simulations and Biomembranes written by Mark S P Sansom and published by Royal Society of Chemistry. This book was released on 2010-08-01 with total page 331 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Machine Learning in Biomolecular Simulations by : Gennady Verkhivker
Download or read book Machine Learning in Biomolecular Simulations written by Gennady Verkhivker and published by Frontiers Media SA. This book was released on 2019-10-21 with total page 129 pages. Available in PDF, EPUB and Kindle. Book excerpt: Machine learning methods such as neural networks, non-linear dimensionality reduction techniques, random forests and others meet in this research topic with biomolecular simulations. The authors of eight articles applied these methods to analyze simulation results, accelerate simulations or to make molecular mechanics force fields more accurate.
Book Synopsis The Monte Carlo Approach To Biopolymers And Protein Folding by : Peter Grassberger
Download or read book The Monte Carlo Approach To Biopolymers And Protein Folding written by Peter Grassberger and published by World Scientific. This book was released on 1998-11-06 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: Information on our detailed genetic code is increasing at a dramatic pace. We need to understand how that is translated into the three-dimensional structure of proteins in order to make use of the information. Progress in this field is hampered by the lack of precise force fields and of efficient codes for finding equilibrium configurations of heteropolymers. However, there has been rapid advance in recent years, and this volume discusses that.
Book Synopsis Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 1 by : Mauro Ferrario
Download or read book Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 1 written by Mauro Ferrario and published by Springer. This book was released on 2007-03-09 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensive collection of lectures by leading experts in the field introduces and reviews all relevant computer simulation methods and their applications in condensed matter systems. Volume 1 is an in-depth introduction to a vast spectrum of computational techniques for statistical mechanical systems of condensed matter. Volume 2 is a collection of state-of-the-art surveys on numerical experiments carried out for a great number of systems.
Book Synopsis The Tight Junction and Its Proteins: More Than Just a Barrier by : Michael Fromm
Download or read book The Tight Junction and Its Proteins: More Than Just a Barrier written by Michael Fromm and published by MDPI. This book was released on 2020-11-20 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: For a long time, the tight junction (TJ) was known to form and regulate the paracellular barrier between epithelia and endothelial cell sheets. Starting shortly after the discovery of the proteins forming the TJ—mainly the two families of claudins and TAMPs—several other functions have been discovered, a striking one being the surprising finding that some claudins form paracellular channels for small ions and/or water. This Special Issue includes 43 articles covering numerous dedicated topics including pathogens affecting the TJ barrier, TJ regulation via immune cells, the TJ as a therapeutic target, TJ and cell polarity, function and regulation by proteins of the tricellular TJ, TJ as a regulator of cellular processes, organ- and tissue-specific functions, TJ as sensors and reacting to environmental conditions, and last but not least, TJ proteins and cancer.
Book Synopsis Protein-Protein Interactions by : Weibo Cai
Download or read book Protein-Protein Interactions written by Weibo Cai and published by BoD – Books on Demand. This book was released on 2012-03-30 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are indispensable players in virtually all biological events. The functions of proteins are coordinated through intricate regulatory networks of transient protein-protein interactions (PPIs). To predict and/or study PPIs, a wide variety of techniques have been developed over the last several decades. Many in vitro and in vivo assays have been implemented to explore the mechanism of these ubiquitous interactions. However, despite significant advances in these experimental approaches, many limitations exist such as false-positives/false-negatives, difficulty in obtaining crystal structures of proteins, challenges in the detection of transient PPI, among others. To overcome these limitations, many computational approaches have been developed which are becoming increasingly widely used to facilitate the investigation of PPIs. This book has gathered an ensemble of experts in the field, in 22 chapters, which have been broadly categorized into Computational Approaches, Experimental Approaches, and Others.
Book Synopsis Multi-Agent-Based Simulations Applied to Biological and Environmental Systems by : Adamatti, Diana Francisca
Download or read book Multi-Agent-Based Simulations Applied to Biological and Environmental Systems written by Adamatti, Diana Francisca and published by IGI Global. This book was released on 2016-12-12 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: The discovery and development of new computational methods have expanded the capabilities and uses of simulations. With agent-based models, the applications of computer simulations are significantly enhanced. Multi-Agent-Based Simulations Applied to Biological and Environmental Systems is a pivotal reference source for the latest research on the implementation of autonomous agents in computer simulation paradigms. Featuring extensive coverage on relevant applications, such as biodiversity conservation, pollution reduction, and environmental risk assessment, this publication is an ideal source for researchers, academics, engineers, practitioners, and professionals seeking material on various issues surrounding the use of agent-based simulations.
Book Synopsis Biomolecules’ Conformational Changes Studied by Simulations and Enhanced Sampling by : Yui Tik (Andrew) Pang
Download or read book Biomolecules’ Conformational Changes Studied by Simulations and Enhanced Sampling written by Yui Tik (Andrew) Pang and published by Springer Nature. This book was released on with total page 104 pages. Available in PDF, EPUB and Kindle. Book excerpt:
