The mapping problem in coarse-grained modelling of biomolecules
Author:
Publisher: Marco Giulini
Published: 2022-05-16
Total Pages: 174
ISBN-13:
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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes
Author: Adam Liwo
Publisher: Springer
Published: 2018-12-19
Total Pages: 849
ISBN-13: 3319958437
DOWNLOAD EBOOKThis 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.
Chemical Theory and Multiscale Simulation in Biomolecules
Author: Guohui Li
Publisher: Elsevier
Published: 2024-03-29
Total Pages: 399
ISBN-13: 0323959180
DOWNLOAD EBOOKChemical 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
Coarse-Grained Modeling of Biomolecules
Author: Garegin A. Papoian
Publisher: CRC Press
Published: 2017-10-30
Total Pages: 430
ISBN-13: 1466576170
DOWNLOAD EBOOK"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.
Principles of Multiscale Modeling
Author: Weinan E
Publisher: Cambridge University Press
Published: 2011-07-07
Total Pages: 485
ISBN-13: 1107096545
DOWNLOAD EBOOKA systematic discussion of the fundamental principles, written by a leading contributor to the field.
Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events
Author: Fabio Trovato
Publisher: Frontiers Media SA
Published: 2022-01-11
Total Pages: 322
ISBN-13: 2889740250
DOWNLOAD EBOOKMachine Learning Methodologies To Study Molecular Interactions
Author: Elif Ozkirimli
Publisher: Frontiers Media SA
Published: 2022-01-21
Total Pages: 147
ISBN-13: 2889741214
DOWNLOAD EBOOKDr. 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.
Coarse-Graining of Condensed Phase and Biomolecular Systems
Author: Gregory A. Voth
Publisher: CRC Press
Published: 2008-09-22
Total Pages: 492
ISBN-13: 1420059564
DOWNLOAD EBOOKExploring 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.
Advance in Structural Bioinformatics
Author: Dongqing Wei
Publisher: Springer
Published: 2014-11-11
Total Pages: 380
ISBN-13: 9401792453
DOWNLOAD EBOOKThis 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.
Distance Geometry
Author: Antonio Mucherino
Publisher: Springer
Published: 2015-01-28
Total Pages: 0
ISBN-13: 9781489985781
DOWNLOAD EBOOKThis 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.
