Computational Methods To Study The Structure And Dynamics Of Biomolecules And Biomolecular Processes

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

Author : Adam Liwo
Publisher : Springer
ISBN 13 : 3319958437
Total Pages : 851 pages
Book Rating : 4.3/5 (199 download)

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Book Synopsis Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by : Adam Liwo

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 851 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.

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

Author : Adam Liwo
Publisher :
ISBN 13 : 9783319958446
Total Pages : pages
Book Rating : 4.9/5 (584 download)

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Book Synopsis Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by : Adam Liwo

Download or read book Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes written by Adam Liwo and published by . This book was released on 2019 with total page 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.

Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly

Author :
Publisher : Academic Press
ISBN 13 : 0128211377
Total Pages : 554 pages
Book Rating : 4.1/5 (282 download)

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Book Synopsis Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly by :

Download or read book Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly written by and published by Academic Press. This book was released on 2020-03-05 with total page 554 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, Volume 170 in the Progress in Molecular Biology and Translational Science series, provides the most topical, informative and exciting monographs available on a wide variety of research topics. The series includes in-depth knowledge on the molecular biological aspects of organismal physiology, with this release including chapters on Pairwise-Additive and Polarizable Atomistic Force Fields for Molecular Dynamics Simulations of Proteins, Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers, Enhanced sampling and free energy methods, and much more. Includes comprehensive coverage on molecular biology Presents ample use of tables, diagrams, schemata and color figures to enhance the reader's ability to rapidly grasp the information provided Contains contributions from renowned experts in the field

Computer Simulation of Biomolecular Systems

Author : W.F. van Gunsteren
Publisher : Springer Science & Business Media
ISBN 13 : 9789072199256
Total Pages : 664 pages
Book Rating : 4.1/5 (992 download)

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Book Synopsis Computer Simulation of Biomolecular Systems by : W.F. van Gunsteren

Download or read book Computer Simulation of Biomolecular Systems written by W.F. van Gunsteren and published by Springer Science & Business Media. This book was released on 1997-11-30 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Modelling Molecular Structure and Reactivity in Biological Systems

Author : Kevin Naidoo
Publisher : Royal Society of Chemistry
ISBN 13 : 1847555373
Total Pages : 304 pages
Book Rating : 4.8/5 (475 download)

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Book Synopsis Modelling Molecular Structure and Reactivity in Biological Systems by : Kevin Naidoo

Download or read book Modelling Molecular Structure and Reactivity in Biological Systems written by Kevin Naidoo and published by Royal Society of Chemistry. This book was released on 2007-10-31 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational and theoretical tools for understanding biological processes at the molecular level is an exciting and innovative area of science. Using these methods to study the structure, dynamics and reactivity of biomacromolecules in solution, computational chemistry is becoming an essential tool, complementing the more traditional methods for structure and reactivity determination. Modelling Molecular Structure and Reactivity in Biological Systems covers three main areas in computational chemistry; structure (conformational and electronic), reactivity and design. Initial sections focus on the link between computational and spectroscopic methods in the investigation of electronic structure. The use of Free Energy calculations for the elucidation of reaction mechanisms in enzymatic systems is also discussed. Subsequent sections focus on drug design and the use of database methods to determine ADME (absorption, distribution, metabolism, excretion) properties. This book provides a complete reference on state of the art computational chemistry practised on biological systems. It is ideal for researchers in the field of computational chemistry interested in its application to biological systems.

Amide Bond Activation

Author : Michal Szostak
Publisher : MDPI
ISBN 13 : 3039212036
Total Pages : 466 pages
Book Rating : 4.0/5 (392 download)

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Book Synopsis Amide Bond Activation by : Michal Szostak

Download or read book Amide Bond Activation written by Michal Szostak and published by MDPI. This book was released on 2019-07-12 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: The amide bond represents a privileged motif in chemistry. The recent years have witnessed an explosion of interest in the development of new chemical transformations of amides. These developments cover an impressive range of catalytic N–C bond activation in electrophilic, Lewis acid, radical, and nucleophilic reaction pathways, among other transformations. Equally relevant are structural and theoretical studies that provide the basis for chemoselective manipulation of amidic resonance. This monograph on amide bonds offers a broad survey of recent advances in activation of amides and addresses various approaches in the field.

Biomimetic Lipid Membranes: Fundamentals, Applications, and Commercialization

Author : Fatma N. Kök
Publisher : Springer
ISBN 13 : 3030115968
Total Pages : 306 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis Biomimetic Lipid Membranes: Fundamentals, Applications, and Commercialization by : Fatma N. Kök

Download or read book Biomimetic Lipid Membranes: Fundamentals, Applications, and Commercialization written by Fatma N. Kök and published by Springer. This book was released on 2019-04-16 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book compiles the fundamentals, applications and viable product strategies of biomimetic lipid membranes into a single, comprehensive source. It broadens its perspective to interdisciplinary realms incorporating medicine, biology, physics, chemistry, materials science, as well as engineering and pharmacy at large. The book guides readers from membrane structure and models to biophysical chemistry and functionalization of membrane surfaces. It then takes the reader through a myriad of surface-sensitive techniques before delving into cutting-edge applications that could help inspire new research directions. With more than half the world's drugs and various toxins targeting these crucial structures, the book addresses a topic of major importance in the field of medicine, particularly biosensor design, diagnostic tool development, vaccine formulation, micro/nano-array systems, and drug screening/development. Provides fundamental knowledge on biomimetic lipid membranes; Addresses some of biomimetic membrane types, preparation methods, properties and characterization techniques; Explains state-of-art technological developments that incorporate microfluidic systems, array technologies, lab-on-a-chip-tools, biosensing, and bioprinting techniques; Describes the integration of biomimetic membranes with current top-notch tools and platforms; Examines applications in medicine, pharmaceutical industry, and environmental monitoring.

Oligomerization in Health and Disease: From Enzymes to G Protein-Coupled Receptors

Author :
Publisher : Academic Press
ISBN 13 : 0128179295
Total Pages : 348 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Oligomerization in Health and Disease: From Enzymes to G Protein-Coupled Receptors by :

Download or read book Oligomerization in Health and Disease: From Enzymes to G Protein-Coupled Receptors written by and published by Academic Press. This book was released on 2020-01-31 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Oligomerization in Health and Disease: From Enzymes to G Protein-Coupled Receptors, Volume 169 in the Progress in Molecular Biology and Translational Science series, provides in-depth reviews on topics of exceptional scienti?c importance. Topics of note in this new release include Computational prediction and re-design of aberrant oligomerization, Oligomerization of G protein-coupled receptors: an historical overview, Prediction and targeting of GPCR oligomer interfaces, GPCR Oligomerization dynamics: Functional consequences, GPCR heteromerization in neuropsychiatric disorders, Structural basis of regulation and oligomerization of human cystathionine ?-synthase, and Oligomerization of Porphobilinogen Synthase. Includes comprehensive coverage of molecular biology Presents ample use of tables, diagrams, schemata and color figures to enhance the reader's ability to rapidly grasp the information provided Contains contributions from renowned experts in the field of molecular biology

Practical Aspects of Computational Chemistry V

Author : Jerzy Leszczynski
Publisher : Springer Nature
ISBN 13 : 3030832449
Total Pages : 292 pages
Book Rating : 4.0/5 (38 download)

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Book Synopsis Practical Aspects of Computational Chemistry V by : Jerzy Leszczynski

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.

Medical Imaging: Concepts, Methodologies, Tools, and Applications

Author : Management Association, Information Resources
Publisher : IGI Global
ISBN 13 : 1522505725
Total Pages : 2081 pages
Book Rating : 4.5/5 (225 download)

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Book Synopsis Medical Imaging: Concepts, Methodologies, Tools, and Applications by : Management Association, Information Resources

Download or read book Medical Imaging: Concepts, Methodologies, Tools, and Applications written by Management Association, Information Resources and published by IGI Global. This book was released on 2016-07-18 with total page 2081 pages. Available in PDF, EPUB and Kindle. Book excerpt: Medical imaging has transformed the ways in which various conditions, injuries, and diseases are identified, monitored, and treated. As various types of digital visual representations continue to advance and improve, new opportunities for their use in medical practice will likewise evolve. Medical Imaging: Concepts, Methodologies, Tools, and Applications presents a compendium of research on digital imaging technologies in a variety of healthcare settings. This multi-volume work contains practical examples of implementation, emerging trends, case studies, and technological innovations essential for using imaging technologies for making medical decisions. This comprehensive publication is an essential resource for medical practitioners, digital imaging technologists, researchers, and medical students.

From Globular Proteins to Amyloids

Author : Irena Roterman-Konieczna
Publisher : Elsevier
ISBN 13 : 0081029829
Total Pages : 280 pages
Book Rating : 4.0/5 (81 download)

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Book Synopsis From Globular Proteins to Amyloids by : Irena Roterman-Konieczna

Download or read book From Globular Proteins to Amyloids written by Irena Roterman-Konieczna and published by Elsevier. This book was released on 2019-10-15 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: From Globular Proteins to Amyloids proposes a model and mechanism for explaining protein misfolding. Concepts presented are based on a model originally intended to show how proteins attain their native conformations. This model is quantitative in nature and founded upon arguments derived from information theory. It facilitates prediction and simulation of the amyloid fibrillation process, also identifying the progressive changes that occur in native proteins that lead to the emergence of amyloid aggregations. Introduces basic rules for protein folding, along with the conditions that result in misfolding Presents research that lies in treating the aqueous environment as a continuum rather than a set of individual water molecules (i.e. the classic representation) Provides practical applications for helping the prevention of amyloidosis and improving drug design

Abridged Thermodynamic and Thermochemical Tables

Author : Frederick Douglas Hamblin
Publisher : Pergamon
ISBN 13 : 0081029810
Total Pages : 278 pages
Book Rating : 4.0/5 (81 download)

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Book Synopsis Abridged Thermodynamic and Thermochemical Tables by : Frederick Douglas Hamblin

Download or read book Abridged Thermodynamic and Thermochemical Tables written by Frederick Douglas Hamblin and published by Pergamon. This book was released on 1968 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: The phenomenon of amyloidosis has attracted the attention of numerous researchers for two main reasons: (1) it involves unexpected changes in protein conformation (without chemical intervention) and (2) has practical implications, such as elucidating the mechanisms which drive neurodegenerative diseases carries. In particular, understanding the process of amyloidosis is a fundamental prerequisite in the search for new, effective drugs and therapies targeting the key area of neurodegenerative diseases. The book proposes a model and a mechanism which explain protein misfolding. The concepts presented are based on a model originally intended to show how proteins attain their native conformations. The model is quantitative in nature and founded upon arguments derived from information theory. It facilitates prediction and simulation of the amyloid fibrillation process. It also identifies progressive changes which occur in native proteins, leading to the emergence of amyloid aggregations.

Mechanics of Biological Systems and Materials & Micro-and Nanomechanics, Volume 4

Author : Martha E. Grady
Publisher : Springer Nature
ISBN 13 : 3030300137
Total Pages : 92 pages
Book Rating : 4.0/5 (33 download)

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Book Synopsis Mechanics of Biological Systems and Materials & Micro-and Nanomechanics, Volume 4 by : Martha E. Grady

Download or read book Mechanics of Biological Systems and Materials & Micro-and Nanomechanics, Volume 4 written by Martha E. Grady and published by Springer Nature. This book was released on 2019-11-09 with total page 92 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mechanics of Biological Systems and Materials & Micro-and Nanomechanics, Volume 4 of the Proceedings of the 2019 SEM Annual Conference & Exposition on Experimental and Applied Mechanics, the fourth volume of six from the Conference, brings together contributions to important areas of research and engineering. The collection presents early findings and case studies on a wide range of topics, including: Extreme NanomechanicsIn-Situ NanomechanicsExpanding Boundaries in MetrologyMicro and Nanoscale DeformationMEMS for Actuation, Sensing and Characterization1D & 2D MaterialsCardiac MechanicsCell Mechanics Biofilms and Microbe MechanicsTraumatic Brain InjuryOrthopedic BiomechanicsLigaments and Soft Materials

Homology Modeling

Author : Sławomir Filipek
Publisher : Springer Nature
ISBN 13 : 1071629743
Total Pages : 379 pages
Book Rating : 4.0/5 (716 download)

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Book Synopsis Homology Modeling by : Sławomir Filipek

Download or read book Homology Modeling written by Sławomir Filipek and published by Springer Nature. This book was released on 2023-03-23 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume provides state-of-the-art methodologies and reviews of important topics in the field of homology modeling. From homology modeling in the twilight zone and improving accuracy through sequence space analysis to approaches to construct multi-protein complex models, the book explores a wide variety of uses and applications of this valuable technique. Written for the highly successful Methods in Molecular Biology series, the chapters include introductions to their respective topics, lists of the necessary programs, webservers, and databases, step-by-step and readily reproducible protocols, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Homology Modeling: Methods and Protocols serves as an ideal guide to recent homology modeling procedures, assumptions made, and model quality assessment that will illuminate the black box of homology modeling for novice readers and broaden the knowledge of this methodology for professionals.

Computation of Biomolecular Structures

Author : Dikeos M. Soumpasis
Publisher : Springer Science & Business Media
ISBN 13 : 3642777988
Total Pages : 250 pages
Book Rating : 4.6/5 (427 download)

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Book Synopsis Computation of Biomolecular Structures by : Dikeos M. Soumpasis

Download or read book Computation of Biomolecular Structures written by Dikeos M. Soumpasis and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 250 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational techniques have become an indispensable part of Molecular Biology, Biochemistry, and Molecular Design. In conjunction with refined experimental methods and powerful hardware, they enable us to analyze and visualize biomolecular structures, simulate their motions and to a variable degree understand their physicochemical properties and function. In addition, they provide essentially the only way to analyze and correlate the astronomical amounts of experimental sequence and structural data accumulating in international databases. We have good reasons to believe that further advances in this area will eventually enable us to predict with sufficient accuracy many structural and functional properties of fairly large biomolecules, given their sequence and specified environmental conditions. However, it is also important to realize that in achieving this goal, we encounter several serious problems of conceptual and methodological nature, the solution of which requires new approaches and algorithms. For example, we need better force fields, more efficient optimization routines, an adequate description of electrostatics and hydration, reliable methods to compute free energies, and ways to extent the length of molecular dynamics simulations by several orders of magnitude.

Coronavirus Drug Discovery

Author : Chukwuebuka Egbuna
Publisher : Elsevier
ISBN 13 : 0323955797
Total Pages : 408 pages
Book Rating : 4.3/5 (239 download)

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Book Synopsis Coronavirus Drug Discovery by : Chukwuebuka Egbuna

Download or read book Coronavirus Drug Discovery written by Chukwuebuka Egbuna and published by Elsevier. This book was released on 2022-07-06 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: Coronavirus Drug Discovery, Volume Three: Druggable Targets and In Silico Update presents comprehensive information on drug discovery against COVID-19. Chapters in Part One of this volume describe the various druggable targets and associated signaling pathways for effective targeting of SARS-CoV-2. In Part Two, chapters discuss the various computational approaches and in silico studies against SARS-CoV-2. Written by global team of experts, this book is an excellent resource that will be extremely useful to drug developers, medicinal chemists, pharmaceutical companies in R&D, research institutes in both academia and industry, and the National Library of Medicines and Health. In addition, agencies such as the National Institutes of Health, Centers for Disease Control and Prevention, World Health Organization, European Medicines Agency, the US Food and Drug Administration, and all others involved in drug discovery against COVID-19 will find this book useful. Discusses the pathogenic mechanisms of SARS-CoV-2 and druggable targets Reviews the various signaling pathways associated with SAR-CoV-2 as possible druggable targets Presents computational approaches and in silico studies against SARS-CoV-2

Dancing Protein Clouds: Intrinsically Disordered Proteins in Health and Disease, Part B

Author :
Publisher : Academic Press
ISBN 13 : 0128226048
Total Pages : 402 pages
Book Rating : 4.1/5 (282 download)

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Book Synopsis Dancing Protein Clouds: Intrinsically Disordered Proteins in Health and Disease, Part B by :

Download or read book Dancing Protein Clouds: Intrinsically Disordered Proteins in Health and Disease, Part B written by and published by Academic Press. This book was released on 2020-08-19 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dancing Protein Clouds: Intrinsically Disordered Proteins in Health and Disease, Part B, represents a set of selected studies on a variety of research topics related to intrinsically disordered proteins. Topics in this update include structural and functional characterization of several important intrinsically disordered proteins, such as 14-3-3 proteins and their partners, as well as proteins from muscle sarcomere; representation of intrinsic disorder-related concept of protein structure-function continuum; discussion of the role of intrinsic disorder in phenotypic switching; consideration of the role of intrinsically disordered proteins in the pathogenesis of neurodegenerative diseases and cancer; discussion of the roles of intrinsic disorder in functional amyloids; demonstration of the usefulness of the analysis of translational diffusion of unfolded and intrinsically disordered proteins; consideration of various computational tools for evaluation of functions of intrinsically disordered regions; and discussion of the role of shear stress in the amyloid formation of intrinsically disordered regions in the brain. Provides some recent studies on the intrinsically disordered proteins and their functions, as well as on the involvement of intrinsically disordered proteins in pthogenesis of various diseases Contains numerous illustrative materials (color figures, diagrams, and tables) to help the readers to delve in the information provided Includes contributions from recognized experts in the field