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Author : Zhongjie Liang,Adolfo Poma,Kurt Kremer,Kei-ichi Okazaki,Sergio Pantano,Simón Poblete
Publisher : Frontiers Media SA
Page : 105 pages
File Size : 40,8 Mb
Release : 2023-05-03
Category : Science
ISBN : 9782832522547
Author : Benoit Roux
Publisher : World Scientific
Page : 209 pages
File Size : 46,6 Mb
Release : 2021-08-23
Category : Computers
ISBN : 9789811232770
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).
Author : Jean-Louis Rivail,Manuel Ruiz-Lopez,Xavier Assfeld
Publisher : Springer
Page : 523 pages
File Size : 51,7 Mb
Release : 2015-10-13
Category : Science
ISBN : 9783319216263
This multi-author contributed volume includes methodological advances and original applications to actual chemical or biochemical phenomena which were not possible before the increased sophistication of modern computers. The chapters contain detailed reviews of the developments of various computational techniques, used to study complex molecular systems such as molecular liquids and solutions (particularly aqueous solutions), liquid-gas, solid-gas interphase and biomacromolecular systems. Quantum modeling of complex molecular systems is a useful resource for graduate students and fledgling researchers and is also an excellent companion for research professionals engaged in computational chemistry, material science, nanotechnology, physics, drug design, and molecular biochemistry.
Author : W.F. van Gunsteren,P.K. Weiner,A.J. Wilkinson
Publisher : Springer Science & Business Media
Page : 664 pages
File Size : 48,6 Mb
Release : 1997-11-30
Category : Science
ISBN : 9072199251
This book is the third volume in this highly successful series. Since the first volume in 1989 and the second in 1993, many exciting developments have occurred in the development of simulation techniques and their application to key biological problems such as protein folding, protein structure prediction and structure-based design, and in how, by combining experimental and theoretical approaches, very large biological systems can be studied at the molecular level. This series attempts to capture that progress. Volume 3 includes contributions that highlight developments in methodology which enable longer and more realistic simulations (e.g. multiple time steps and variable reduction techniques), a study of force fields for proteins and new force field development, a novel approach to the description of molecular shape and the use of molecular shape descriptors, the study of condensed phase chemical reactions, the use of electrostatic techniques in the study of protonation, equilibria and flexible docking studies, structure refinement using experimental data (X-ray, NMR, neutron, infrared) and theoretical methods (solvation models, normal mode analysis, MD simulations, MC lattice dynamics, and knowledge-based potentials). There are several chapters that show progress in the development of methodologies for the study of folding processes, binding affinities, and the prediction of ligand-protein complexes. The chapters, contributed by experienced researchers, many of whom are leaders in their field of study, are organised to cover developments in: simulation methodology the treatment of electrostatics protein structure refinement the combined experimental and theoretical approaches to the study of very large biological systems applications and methodology involved in the study of protein folding applications and methodology associated with structure-based design.
Author : Tamar Schlick
Publisher : Royal Society of Chemistry
Page : 354 pages
File Size : 40,6 Mb
Release : 2012-05-24
Category : Science
ISBN : 9781849735056
The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.
Author : Benoît Roux
Publisher : Unknown
Page : 209 pages
File Size : 45,8 Mb
Release : 2021
Category : Electronic books
ISBN : 9811232768
Author : Yong Wang,Ruhong Zhou
Publisher : Unknown
Page : 0 pages
File Size : 48,7 Mb
Release : 2023
Category : SCIENCE
ISBN : 0735425264
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.
Author : Elson Longo,Felipe de Almeida La Porta
Publisher : Springer
Page : 454 pages
File Size : 45,9 Mb
Release : 2017-07-12
Category : Technology & Engineering
ISBN : 9783319538983
In this book we explore new approaches to understanding the physical and chemical properties of emergent complex functional materials, revealing a close relationship between their structures and properties at the molecular level. The primary focus of this book is on the ability to synthesize materials with a controlled chemical composition, a crystallographic structure, and a well-defined morphology. Special attention is also given to the interplay of theory, simulation and experimental results, in order to interconnect theoretical knowledge and experimental approaches, which can reveal new scientific and technological directions in several fields, expanding the versatility to yield a variety of new complex materials with desirable applications and functions. Some of the challenges and opportunities in this field are also discussed, targeting the development of new emergent complex functional materials with tailored properties to solve problems related to renewable energy, health, and environmental sustainability. A more fundamental understanding of the physical and chemical properties of new emergent complex functional materials is essential to achieving more substantial progress in a number of technological fields. With this goal in mind, the editors invited acknowledged specialists to contribute chapters covering a broad range of disciplines.
Author : Kurt Wuthrich,Bert Weckhuysen,Laurence Rongy,Anne De Wit
Publisher : World Scientific
Page : 372 pages
File Size : 41,8 Mb
Release : 2020-12-21
Category : Science
ISBN : 9789811228223
Chaired by K Wüthrich (Nobel Laureate in Chemistry, 2002) and co-chaired by B Weckhuysen, this by-invitation-only conference has gathered 39 participants — who are leaders in the field of computational modeling and its applications in Chemistry, Material Sciences and Biology. Highlights of the Conference Proceedings are short, prepared statements by all the participants and the records of lively discussions on the current and future perspectives in the field of computational modeling, from chemistry to materials to biology.
Author : David M Close,Jerzy Leszczynski,Michael Meyer
Publisher : World Scientific
Page : 361 pages
File Size : 50,9 Mb
Release : 2003-12-15
Category : Science
ISBN : 9789814483568
The gap between experimental objects and models for calculations in chemistry is being bridged. The size of experimental nano-objects is decreasing, while reliable calculations are feasible for larger and larger molecular systems. The results of these calculations for isolated molecules are becoming more relevant for experiments. However, there are still significant challenges for computational methods. This series of books presents reviews of current advances in computational methodologies and applications.Chapter 1 of this volume provides an overview of the theoretical and numerical aspects in the development of the polarizable continuum model (PCM). Chapter 2 demonstrates a multiplicative scheme used to estimate the properties of two- and three-dimensional clusters from the properties of their one-dimensional components. Chapter 3 discusses the application of ab initio methods for a reliable evaluation of the characteristics of hydrogen-bonded and van der Waals complexes.Ab initio quantum-chemical methods are popular among researchers investigating various aspects of DNA. The properties of DNA base polyads linked by base-base hydrogen bonds are reviewed in Chapter 4, while Chapter 5 reviews the primary radiation-induced defects in nucleic acid building blocks, and how DNA can be influenced by chemical and environmental effects. Finally, Chapter 6 discusses available experimental data of DNA bases, base pairs, and their complexes with water.
Author : Sonsoles Martín-Santamaría
Publisher : Royal Society of Chemistry
Page : 392 pages
File Size : 49,7 Mb
Release : 2017-11-01
Category : Science
ISBN : 9781782627005
This book offers a fresh perspective on how computational tools can aid the chemical biology research community and drive new research.
Author : Ruhong Zhou
Publisher : CRC Press
Page : 392 pages
File Size : 49,6 Mb
Release : 2014-08-21
Category : Science
ISBN : 9781466562950
Although molecular modeling has been around for a while, the groundbreaking advancement of massively parallel supercomputers and novel algorithms for parallelization is shaping this field into an exciting new area. Developments in molecular modeling from experimental and computational techniques have enabled a wide range of biological applications. Responding to this renaissance, Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology includes discussions of advanced techniques of molecular modeling and the latest research advancements in biomolecular applications from leading experts. The book begins with a brief introduction of major methods and applications, then covers the development of cutting-edge methods/algorithms, new polarizable force fields, and massively parallel computing techniques, followed by descriptions of how these novel techniques can be applied in various research areas in molecular biology. It also examines the self-assembly of biomacromolecules, including protein folding, RNA folding, amyloid peptide aggregation, and membrane lipid bilayer formation. Additional topics highlight biomolecular interactions, including protein interactions with DNA/RNA, membrane, ligands, and nanoparticles. Discussion of emerging topics in biomolecular modeling such as DNA sequencing with solid-state nanopores and biological water under nanoconfinement round out the coverage. This timely summary contains the perspectives of leading experts on this transformation in molecular biology and includes state-of-the-art examples of how molecular modeling approaches are being applied to critical questions in modern quantitative biology. It pulls together the latest research and applications of molecular modeling and real-world expertise that can boost your research and development of applications in this rapidly changing field.
Author : Girish Kumar Gupta,Mohammad Hassan Baig
Publisher : Walter de Gruyter GmbH & Co KG
Page : 210 pages
File Size : 49,6 Mb
Release : 2022-05-09
Category : Science
ISBN : 9783110493955
In Silico Chemistry and Biology: Current and Future Prospects provides a compact overview on recent advances in this highly dynamic branch of chemistry. Various methods of protein modelling and computer-assisted drug design are presented, including fragment- and ligand-based approaches. Many successful practical applications of these techniques are demonstrated. The authors also look to the future and describe the main challenges of the field.
Author : Massimiliano Bonomi,Carlo Camilloni
Publisher : Unknown
Page : 581 pages
File Size : 52,7 Mb
Release : 2019
Category : Biochemistry
ISBN : 1493996088
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.
Author : Jerzy Leszczynski,Manoj K. Shukla
Publisher : Springer Nature
Page : 292 pages
File Size : 53,9 Mb
Release : 2021-10-21
Category : Science
ISBN : 9783030832445
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.