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Author: Valerie Daggett
Publisher: Elsevier
Published: 2003-11-26
Total Pages: 477
ISBN-13: 0080493785
DOWNLOAD EBOOKProtein 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
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.
Author: Roger Gregory
Publisher: CRC Press
Published: 2024-11-01
Total Pages: 596
ISBN-13: 1040282512
DOWNLOAD EBOOKThis work covers advances in the interactions of proteins with their solvent environment and provides fundamental physical information useful for the application of proteins in biotechnology and industrial processes. It discusses in detail structure, dynamic and thermodynamic aspects of protein hydration, as well as proteins in aqueous and organic solvents as they relate to protein function, stability and folding.
Author: Francesco L. Gervasio
Publisher: John Wiley & Sons
Published: 2019-04-29
Total Pages: 368
ISBN-13: 3527342656
DOWNLOAD EBOOKA guide to applying the power of modern simulation tools to better drug design Biomolecular Simulations in Structure-based Drug Discovery offers an up-to-date and comprehensive review of modern simulation tools and their applications in real-life drug discovery, for better and quicker results in structure-based drug design. The authors describe common tools used in the biomolecular simulation of drugs and their targets and offer an analysis of the accuracy of the predictions. They also show how to integrate modeling with other experimental data. Filled with numerous case studies from different therapeutic fields, the book helps professionals to quickly adopt these new methods for their current projects. Experts from the pharmaceutical industry and academic institutions present real-life examples for important target classes such as GPCRs, ion channels and amyloids as well as for common challenges in structure-based drug discovery. Biomolecular Simulations in Structure-based Drug Discovery is an important resource that: -Contains a review of the current generation of biomolecular simulation tools that have the robustness and speed that allows them to be used as routine tools by non-specialists -Includes information on the novel methods and strategies for the modeling of drug-target interactions within the framework of real-life drug discovery and development -Offers numerous illustrative case studies from a wide-range of therapeutic fields -Presents an application-oriented reference that is ideal for those working in the various fields Written for medicinal chemists, professionals in the pharmaceutical industry, and pharmaceutical chemists, Biomolecular Simulations in Structure-based Drug Discovery is a comprehensive resource to modern simulation tools that complement and have the potential to complement or replace laboratory assays for better results in drug design.
Author: Slavica Jonic
Publisher: Frontiers Media SA
Published: 2019-01-24
Total Pages: 128
ISBN-13: 2889456994
DOWNLOAD EBOOKModels 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: Michael Feig
Publisher: John Wiley & Sons
Published: 2009-12-09
Total Pages: 334
ISBN-13: 3527629262
DOWNLOAD EBOOKA 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.
Author: Benedict Leimkuhler
Publisher: Springer Science & Business Media
Published: 2006-03-22
Total Pages: 364
ISBN-13: 3540316183
DOWNLOAD EBOOKMolecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.
Author: B. Leimkuhler
Publisher: Springer Science & Business Media
Published: 2006-02-10
Total Pages: 390
ISBN-13: 9783540255420
DOWNLOAD EBOOKMolecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.
Author: Christophe Chipot
Publisher: Springer Science & Business Media
Published: 2007-01-08
Total Pages: 528
ISBN-13: 3540384472
DOWNLOAD EBOOKFree energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.
Author: Minu Elizabeth Thomas
Publisher: Elsevier
Published: 2023-02-28
Total Pages: 628
ISBN-13: 0323909965
DOWNLOAD EBOOKComputational approaches offer researchers unique insights into the structure, characteristics, and properties of macromolecules. However, with applications across a broad range of areas, various methods have been developed for exploring macromolecules in in silico; therefore, it can be difficult for researchers to select the most appropriate method for their specific needs. Covering both biopolymers and synthetic polymers, In-Silico Approaches to Macromolecular Chemistry familiarizes readers with the theoretical tools and software appropriate for such studies. In addition to providing essential background knowledge on both computational tools and macromolecules, the book presents in-depth studies of in silico macromolecule chemistry, discusses and compares these with experimental studies, and highlights the future potential for such approaches. Written by specialists in their respective fields, this book helps students, researchers, and industry professionals gain a clear overview of the field, and furnishes them with the knowledge needed to understand and select the most appropriate tools for conducting and analyzing computational studies. - Highlights in silico studies of both bio and synthetic macromolecules in one book - Supports both learners and experts though a combination of detailed guidance and perspectives on the future potential for in silico approaches to macromolecules - Familiarizes readers with theoretical tools and software helping them select the best approach for their specific needs
