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Author :
Publisher : Marco Giulini
ISBN 13 :
Total Pages : 174 pages
Book Rating : 4./5 ( download)
Download or read book The mapping problem in coarse-grained modelling of biomolecules written by and published by Marco Giulini. This book was released on 2022-05-16 with total page 174 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Adam Liwo
Publisher : Springer
ISBN 13 : 3319958437
Total Pages : 849 pages
Book Rating : 4.3/5 (199 download)
Download or read book Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes written by Adam Liwo and published by Springer. This book was released on 2018-12-19 with total page 849 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Guohui Li
Publisher : Elsevier
ISBN 13 : 0323959180
Total Pages : 399 pages
Book Rating : 4.3/5 (239 download)
Download or read book Chemical Theory and Multiscale Simulation in Biomolecules written by Guohui Li and published by Elsevier. This book was released on 2024-03-29 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical Theory and Multiscale Simulation in Biomolecules: From Principles to Case Studies helps readers understand what simulation is, what information modeling of biomolecules can provide, and how to compare this information with experiments. Beginning with an introduction to computational theory for modeling, the book goes on to describe how to control the conditions of modeling systems and possible strategies for time-cost savings in computation. Part Two further outlines key methods, with step-by-step guidance supporting readers in studying and practicing simulation processes. Part Three then shows how these theories are controlled and applied in practice, through examples and case studies on varied applications. This book is a practical guide for new learners, supporting them in learning and applying molecular modeling in practice, whilst also providing more experienced readers with the knowledge needed to gain a deep understanding of the theoretical background behind key methods. - Presents computational theory alongside case studies to help readers understand the use of simulation in practice - Includes extensive examples of different types of simulation methods and approaches to result analysis - Provides an overview of the current academic frontier and research challenges, encouraging creativity and directing attention to current problems
Author : Garegin A. Papoian
Publisher : CRC Press
ISBN 13 : 1466576170
Total Pages : 430 pages
Book Rating : 4.4/5 (665 download)
Download or read book Coarse-Grained Modeling of Biomolecules written by Garegin A. Papoian and published by CRC Press. This book was released on 2017-10-30 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt: "The chapters in this book survey the progress in simulating biomolecular dynamics.... The images conjured up by this work are not yet universally loved, but are beginning to bring new insights into the study of biological structure and function. The future will decide whether this scientific movement can bring forth its Picasso or Modigliani." –from the Foreword by Peter G. Wolynes, Bullard-Welch Foundation Professor of Science, Rice University This book highlights the state-of-art in coarse-grained modeling of biomolecules, covering both fundamentals as well as various cutting edge applications. Coarse-graining of biomolecules is an area of rapid advances, with numerous new force fields having appeared recently and significant progress made in developing a systematic theory of coarse-graining. The contents start with first fundamental principles based on physics, then survey specific state-of-art coarse-grained force fields of proteins and nucleic acids, and provide examples of exciting biological problems that are at large scale, and hence, only amenable to coarse-grained modeling. Introduces coarse-grained models of proteins and nucleic acids. Showcases applications such as genome packaging in nuclei and understanding ribosome dynamics Gives the physical foundations of coarse-graining Demonstrates use of models for large-scale assemblies in modern studies Garegin A. Papoian is the first Monroe Martin Associate Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology at the University of Maryland.
Author : Weinan E
Publisher : Cambridge University Press
ISBN 13 : 1107096545
Total Pages : 485 pages
Book Rating : 4.1/5 (7 download)
Download or read book Principles of Multiscale Modeling written by Weinan E and published by Cambridge University Press. This book was released on 2011-07-07 with total page 485 pages. Available in PDF, EPUB and Kindle. Book excerpt: A systematic discussion of the fundamental principles, written by a leading contributor to the field.
Author : Fabio Trovato
Publisher : Frontiers Media SA
ISBN 13 : 2889740250
Total Pages : 322 pages
Book Rating : 4.8/5 (897 download)
Download or read book Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events written by Fabio Trovato and published by Frontiers Media SA. This book was released on 2022-01-11 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Elif Ozkirimli
Publisher : Frontiers Media SA
ISBN 13 : 2889741214
Total Pages : 147 pages
Book Rating : 4.8/5 (897 download)
Download or read book Machine Learning Methodologies To Study Molecular Interactions written by Elif Ozkirimli and published by Frontiers Media SA. This book was released on 2022-01-21 with total page 147 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dr. Elif Ozkirimli is a full time employee of F. Hoffmann-La Roche AG, Switzerland and Dr. Artur Yakimovich is a full time employee of Roche Products Limited, UK. All other Topic Editors declare no competing interests with regards to the Research Topic.
Author : Gregory A. Voth
Publisher : CRC Press
ISBN 13 : 1420059564
Total Pages : 492 pages
Book Rating : 4.4/5 (2 download)
Download or read book Coarse-Graining of Condensed Phase and Biomolecular Systems written by Gregory A. Voth and published by CRC Press. This book was released on 2008-09-22 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exploring recent developments in the field, Coarse-Graining of Condensed Phase and Biomolecular Systems examines systematic ways of constructing coarse-grained representations for complex systems. It explains how this approach can be used in the simulation and modeling of condensed phase and biomolecular systems. Assembling some of the most influential, world-renowned researchers in the field, this book covers the latest developments in the coarse-grained molecular dynamics simulation and modeling of condensed phase and biomolecular systems. Each chapter focuses on specific examples of evolving coarse-graining methodologies and presents results for a variety of complex systems. The contributors discuss the minimalist, inversion, and multiscale approaches to coarse-graining, along with the emerging challenges of coarse-graining. They also connect atomic-level information with new coarse-grained representations of complex systems, such as lipid bilayers, proteins, peptides, and DNA.
Author : Dongqing Wei
Publisher : Springer
ISBN 13 : 9401792453
Total Pages : 380 pages
Book Rating : 4.4/5 (17 download)
Download or read book Advance in Structural Bioinformatics written by Dongqing Wei and published by Springer. This book was released on 2014-11-11 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conformation searches. This book will be of immense value to researchers and students in the fields of bioinformatics, computational biology and chemistry. Dr. Dongqing Wei is a Professor at the Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, China. His research interest is in the general area of structural bioinformatics.
Author : Antonio Mucherino
Publisher : Springer
ISBN 13 : 9781489985781
Total Pages : 0 pages
Book Rating : 4.9/5 (857 download)
Download or read book Distance Geometry written by Antonio Mucherino and published by Springer. This book was released on 2015-01-28 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a collection of research surveys on the Distance Geometry Problem (DGP) and its applications. It will be divided into three parts: Theory, Methods and Applications. Each part will contain at least one survey and several research papers. The first part, Theory, will deal with theoretical aspects of the DGP, including a new class of problems and the study of its complexities as well as the relation between DGP and other related topics, such as: distance matrix theory, Euclidean distance matrix completion problem, multispherical structure of distance matrices, distance geometry and geometric algebra, algebraic distance geometry theory, visualization of K-dimensional structures in the plane, graph rigidity, and theory of discretizable DGP: symmetry and complexity. The second part, Methods, will discuss mathematical and computational properties of methods developed to the problems considered in the first chapter including continuous methods (based on Gaussian and hyperbolic smoothing, difference of convex functions, semidefinite programming, branch-and-bound), discrete methods (based on branch-and-prune, geometric build-up, graph rigidity), and also heuristics methods (based on simulated annealing, genetic algorithms, tabu search, variable neighborhood search). Applications will comprise the third part and will consider applications of DGP to NMR structure calculation, rational drug design, molecular dynamics simulations, graph drawing and sensor network localization. This volume will be the first edited book on distance geometry and applications. The editors are in correspondence with the major contributors to the field of distance geometry, including important research centers in molecular biology such as Institut Pasteur in Paris.
Author : Yashwant Pathak
Publisher : CRC Press
ISBN 13 : 1000952754
Total Pages : 275 pages
Book Rating : 4.0/5 (9 download)
Download or read book Artificial Intelligence in Bioinformatics and Chemoinformatics written by Yashwant Pathak and published by CRC Press. This book was released on 2023-10-11 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: The authors aim to shed light on the practicality of using machine learning in finding complex chemoinformatics and bioinformatics applications as well as identifiying AI in biological and chemical data points. The chapters are designed in such a way that they highlight the important role of AI in chemistry and bioinformatics particularly for the classification of diseases, selection of features and compounds, dimensionality reduction and more. In addition, they assist in the organization and optimal use of data points generated from experiments performed using AI techniques. This volume discusses the development of automated tools and techniques to aid in research plans. Features Covers AI applications in bioinformatics and chemoinformatics Demystifies the involvement of AI in generating biological and chemical data Provides an Introduction to basic and advanced chemoinformatics computational tools Presents a chemical biology based toolset for artificial intelligence usage in drug design Discusses computational methods in cancer, genome mapping, and stem cell research
Author :
Publisher : Academic Press
ISBN 13 : 0128007893
Total Pages : 331 pages
Book Rating : 4.1/5 (28 download)
Download or read book Biomolecular Modelling and Simulations written by and published by Academic Press. This book was released on 2014-10-11 with total page 331 pages. Available in PDF, EPUB and Kindle. Book excerpt: Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology series is the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins. Each thematically organized volume is guest edited by leading experts in a broad range of protein-related topics. - Describes advances in biomolecular modelling and simulations - Chapters are written by authorities in their field - Targeted to a wide audience of researchers, specialists, and students - The information provided in the volume is well supported by a number of high quality illustrations, figures, and tables
Author : Marta Filizola
Publisher : Springer Science & Business Media
ISBN 13 : 9400774230
Total Pages : 228 pages
Book Rating : 4.4/5 (7 download)
Download or read book G Protein-Coupled Receptors - Modeling and Simulation written by Marta Filizola and published by Springer Science & Business Media. This book was released on 2013-10-25 with total page 228 pages. Available in PDF, EPUB and Kindle. Book excerpt: G protein-coupled receptors (GPCRs) are heptahelical transmembrane receptors that convert extra-cellular stimuli into intra-cellular signaling, and ultimately into biological responses. Since GPCRs are natural targets for approximately 40% of all modern medicines, it is not surprising that they have been the subject of intense research. Notwithstanding the amount of data generated over the years, discovering ligands of these receptors with optimal therapeutic properties is not straightforward and has certainly been hampered for years by the lack of high-resolution structural information about these receptors. Luckily, there has been a steady increase of high-resolution crystal structures of these receptors since 2007, and this information, integrated with dynamic inferences from computational and experimental methods, holds great potential for the discovery of new, improved drugs. This book, which provides, for the first time, state-of-the-art views on modeling and simulation of GPCRs, is divided into 4 parts. In the first part, the impact of currently available GPCR crystal structures on structural modeling is discussed extensively as are critical insights from simulations in the second part of the book. The third part reports recent progress in rational ligand discovery and mathematical modeling, whereas the fourth part provides an overview of bioinformatics tools and resources that are available for GPCRs.
Author : Michael P. Allen
Publisher : Oxford University Press
ISBN 13 : 0192524704
Total Pages : 640 pages
Book Rating : 4.1/5 (925 download)
Download or read book Computer Simulation of Liquids written by Michael P. Allen and published by Oxford University Press. This book was released on 2017-08-15 with total page 640 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a practical guide to molecular dynamics and Monte Carlo simulation techniques used in the modelling of simple and complex liquids. Computer simulation is an essential tool in studying the chemistry and physics of condensed matter, complementing and reinforcing both experiment and theory. Simulations provide detailed information about structure and dynamics, essential to understand the many fluid systems that play a key role in our daily lives: polymers, gels, colloidal suspensions, liquid crystals, biological membranes, and glasses. The second edition of this pioneering book aims to explain how simulation programs work, how to use them, and how to interpret the results, with examples of the latest research in this rapidly evolving field. Accompanying programs in Fortran and Python provide practical, hands-on, illustrations of the ideas in the text.
Author : Sidney A. Simon
Publisher : Academic Press
ISBN 13 : 0080925855
Total Pages : 606 pages
Book Rating : 4.0/5 (89 download)
Download or read book Peptide-Lipid Interactions written by Sidney A. Simon and published by Academic Press. This book was released on 2002-11-13 with total page 606 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains a comprehensive overview of peptide-lipid interactions by leading researchers. The first part covers theoretical concepts, experimental considerations, and thermodynamics. The second part presents new results obtained through site-directed EPR, electron microscopy, NMR, isothermal calorimetry, and fluorescence quenching. The final part covers problems of biological interest, including signal transduction, membrane transport, fusion, and adhesion. Key Features * world-renowned experts * state-of-the-art experimental methods * monolayers, bilayers, biological membranes * theoretical aspects and computer simulations * rafts * synaptic transmission * membrane fusion * signal transduction
Author : Slavica Jonic
Publisher : Frontiers Media SA
ISBN 13 : 2889456994
Total Pages : 128 pages
Book Rating : 4.8/5 (894 download)
Download or read book Hybrid Biomolecular Modeling written by Slavica Jonic and published by Frontiers Media SA. This book was released on 2019-01-24 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: Models of biomolecular structure and dynamics are often obtained by combining simulation or prediction approaches (e.g., comparative modeling, Molecular Dynamics (MD) simulations, Normal Mode Analysis (NMA), etc.) with experimental approaches (e.g., Nuclear Magnetic Resonance (NMR), X-ray crystallography, Small-Angle X-ray Scattering (SAXS), Electron Microscopy (EM), etc.). Such hybrid modeling extends the capabilities of experimental techniques, by enriching structural information and facilitating dynamics studies of biomolecules. This eBook contains articles on methodological developments, applications, and challenges of hybrid biomolecular modeling that have been collected in the framework of the Frontiers Research Topic entitled “Hybrid Biomolecular Modeling”.
Author : Jerzy Leszczynski
Publisher : Springer Nature
ISBN 13 : 3030832449
Total Pages : 292 pages
Book Rating : 4.0/5 (38 download)
Download or read book Practical Aspects of Computational Chemistry V written by Jerzy Leszczynski and published by Springer Nature. This book was released on 2021-10-21 with total page 292 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents contributions on a wide range of computational research applied to fields ranging from molecular systems to bulk structures. This volume highlights current trends in modern computational chemistry and discusses the development of theoretical methodologies, state-of-the-art computational algorithms and their practical applications. This volume is part of a continuous effort by the editors to document recent advances by prominent researchers in the area of computational chemistry. Most of the chapters are contributed by invited speakers and participants to International annual conference “Current Trends in Computational Chemistry”, organized by Jerzy Leszczynski, one of the editors of the current volume. This conference series has become an exciting platform for eminent theoretical and computational chemists to discuss their recent findings and is regularly honored by the presence of Nobel laureates. Topics covered in the book include reactive force-field methodologies, coarse-grained modeling, DNA damage radiosensitizers, modeling and simulation of surfaces and interfaces, non-covalent interactions, and many others. The book is intended for theoretical and computational chemists, physical chemists, material scientists and those who are eager to apply computational chemistry methods to problems of chemical and physical importance. It is a valuable resource for undergraduate, graduate and PhD students as well as for established researchers.
