Hybrid Biomolecular Modeling

Hybrid Biomolecular Modeling
Author: Slavica Jonic
Publisher: Frontiers Media SA
Total Pages: 128
Release: 2019-01-24
Genre:
ISBN: 2889456994

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”.

Modeling Solvent Environments

Modeling Solvent Environments
Author: Michael Feig
Publisher: John Wiley & Sons
Total Pages: 334
Release: 2009-12-09
Genre: Science
ISBN: 3527629262

A comprehensive view of the current methods for modeling solvent environments with contributions from the leading researchers in the field. Throughout, the emphasis is placed on the application of such models in simulation studies of biological processes, although the coverage is sufficiently broad to extend to other systems as well. As such, this monograph treats a full range of topics, from statistical mechanics-based approaches to popular mean field formalisms, coarse-grained solvent models, more established explicit, fully atomic solvent models, and recent advances in applying ab initio methods for modeling solvent properties.

Physics at the Biomolecular Interface

Physics at the Biomolecular Interface
Author: Ariel Fernández
Publisher: Springer
Total Pages: 490
Release: 2016-05-11
Genre: Science
ISBN: 3319308521

This book focuses primarily on the role of interfacial forces in understanding biological phenomena at the molecular scale. By providing a suitable statistical mechanical apparatus to handle the biomolecular interface, the book becomes uniquely positioned to address core problems in molecular biophysics. It highlights the importance of interfacial tension in delineating a solution to the protein folding problem, in unravelling the physico-chemical basis of enzyme catalysis and protein associations, and in rationally designing molecular targeted therapies. Thus grounded in fundamental science, the book develops a powerful technological platform for drug discovery, while it is set to inspire scientists at any level in their careers determined to address the major challenges in molecular biophysics. The acknowledgment of how exquisitely the structure and dynamics of proteins and their aqueous environment are related attests to the overdue recognition that biomolecular phenomena cannot be effectively understood without dealing with interfacial behaviour. There is an urge to grasp how biologically relevant behaviour is shaped by the structuring of biomolecular interfaces and how interfacial tension affects the molecular events that take place in the cell. This book squarely addresses these needs from a physicist perspective. The book may serve as a monograph for practitioners and, alternatively, as an advanced textbook. Fruitful reading requires a background in physical chemistry and some basics in biophysics. The selected problems at the end of the chapters and the progression in conceptual difficulty make it a suitable textbook for a graduate level course or an elective course for seniors majoring in chemistry, physics, biomedical engineering or related disciplines.

Enantioselection in Asymmetric Catalysis

Enantioselection in Asymmetric Catalysis
Author: Ilya D. Gridnev
Publisher: CRC Press
Total Pages: 274
Release: 2016-11-03
Genre: Science
ISBN: 1315353342

The field of asymmetric catalysis is currently one of the hottest areas in chemistry. This unique book focuses on the mechanism of enantioselectivity in asymmetric catalysis, rather than asymmetric catalysis from the synthetic view. It describes reliable, experimentally and computationally supported mechanisms, and discusses the danger of so-called "plausible" or "accepted" mechanisms leading to wrong conclusions. It draws parallels to enzymatic catalysis in biochemistry, and examines in detail the physico-chemical aspects of enantioselective catalysis.

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes
Author: Adam Liwo
Publisher: Springer
Total Pages: 849
Release: 2018-12-19
Genre: Technology & Engineering
ISBN: 3319958437

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.

Annual Reports in Computational Chemistry

Annual Reports in Computational Chemistry
Author: David Spellmeyer
Publisher: Elsevier
Total Pages: 347
Release: 2006-11-06
Genre: Science
ISBN: 0080465420

Annual Reports in Computational Chemistry is a new periodical providing timely and critical reviews of important topics in computational chemistry as applied to all chemical disciplines. Topics covered include quantum chemistry, molecular mechanics, force fields, chemical education, and applications in academic and industrial settings. Each volume is organized into (thematic) sections with contributions written by experts. Focusing on the most recent literature and advances in the field, each article covers a specific topic of importance to computational chemists. Annual Reports in Computational Chemistry is a 'must' for researchers and students wishing to stay up-to-date on current developments in computational chemistry.* Broad coverage of computational chemistry and up-to-date information * The topics covered include quantum chemistry, molecular mechanics, force fields, chemical education, and applications in academic and industrial settings * Each chapter reviews the most recent literature on a specific topic of interest to computational chemists

Innovations in Biomolecular Modeling and Simulations

Innovations in Biomolecular Modeling and Simulations
Author: Tamar Schlick
Publisher: Royal Society of Chemistry
Total Pages: 355
Release: 2012
Genre: Science
ISBN: 1849734623

This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts.

Computational Approaches in Physics

Computational Approaches in Physics
Author: Maria Fyta
Publisher: Morgan & Claypool Publishers
Total Pages: 136
Release: 2016-11-01
Genre: Computers
ISBN: 1681744171

Computational Approaches in Physics reviews computational schemes which are used in the simulations of physical systems. These range from very accurate ab initio techniques up to coarse-grained and mesoscopic schemes. The choice of the method is based on the desired accuracy and computational efficiency. A bottom-up approach is used to present the various simulation methods used in Physics, starting from the lower level and the most accurate methods, up to particle-based ones. The book outlines the basic theory underlying each technique and its complexity, addresses the computational implications and issues in the implementation, as well as present representative examples. A link to the most common computational codes, commercial or open source is listed in each chapter. The strengths and deficiencies of the variety of techniques discussed in this book are presented in detail and visualization tools commonly used to make the simulation data more comprehensive are also discussed. In the end, specific techniques are used as bridges across different disciplines. To this end, examples of different systems tackled with the same methods are presented. The appendices include elements of physical theory which are prerequisites in understanding the simulation methods.

Advances in Protein Molecular and Structural Biology Methods

Advances in Protein Molecular and Structural Biology Methods
Author: Timir Tripathi
Publisher: Academic Press
Total Pages: 716
Release: 2022-01-14
Genre: Science
ISBN: 0323902650

Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. - Presents a thorough overview of the latest and emerging methods and technologies for protein study - Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy - Includes computational and machine learning methods - Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins