Large Scale Quantum Mechanical Enzymology

Author by : Greg Lever
Languange : en
Publisher by : Springer
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Description : This work establishes linear-scaling density-functional theory (DFT) as a powerful tool for understanding enzyme catalysis, one that can complement quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics simulations. The thesis reviews benchmark studies demonstrating techniques capable of simulating entire enzymes at the ab initio quantum-mechanical level of accuracy. DFT has transformed the physical sciences by allowing researchers to perform parameter-free quantum-mechanical calculations to predict a broad range of physical and chemical properties of materials. In principle, similar methods could be applied to biological problems. However, even the simplest biological systems contain many thousands of atoms and are characterized by extremely complex configuration spaces associated with a vast number of degrees of freedom. The development of linear-scaling density-functional codes makes biological molecules accessible to quantum-mechanical calculation, but has yet to resolve the complexity of the phase space. Furthermore, these calculations on systems containing up to 2,000 atoms can capture contributions to the energy that are not accounted for in QM/MM methods (for which the Nobel prize in Chemistry was awarded in 2013) and the results presented here reveal profound shortcomings in said methods.


Structural And Mechanistic Enzymology

Author by : Anonim
Languange : en
Publisher by : Academic Press
Format Available : PDF, ePub, Mobi
Total Read : 48
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Description : Both strategies for investigation (computational and experimental) in structural and mechanistic Enzymology have developed to some extent independently. However, over the last few years a trend has emerged for strengthening their integration. This combination not only brings together computations and experiments focused on the same enzymatic problems, but also provides complementary insights into the investigated properties and has a powerful synergy effect. This thematic volume of Advances in Protein Chemistry and Structural Biology focuses on the recent success in structural and mechanistic enzymology and has its main emphasis on explaining the enzyme phenomena by using both the experimental and computational approaches. The selected contributions demonstrate how the application of a variety of experimental techniques and modeling methods helps further the understanding of enzyme dynamics, mechanism, inhibition, and drug design. Focuses on the recent success in structural and mechanistic enzymology Has its main emphasis on explaining the enzyme phenomena by using both the experimental and computational approaches Demonstrates how the application of a variety of experimental techniques and modeling methods helps further the understanding of enzyme dynamics, mechanism, inhibition, and drug design


Enzymology And Molecular Biology Of Carbonyl Metabolism 10

Author by : H. Weiner
Languange : en
Publisher by : Gulf Professional Publishing
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Description : The largest collection of articles on the three major gene families, this work ranges from enzymology to molecular biology to physiological implications. The three gene families are related in that the enzymes catalyse the NAD(P) dependent oxidation or reduction of carbonyl containing substrates. The substrates are important in diverse areas such as alcoholism, diabetes and cancer related problems as well as simple detoxification. The scope of the chapters, contributed by leading international scientists, is wide and covers gene regulation to enzyme mechanisms and protein structure. This is the only publication dealing in such depth with just three gene families. An important reference for researchers in toxicology and molecular biology.


Computational Molecular Modelling In Structural Biology

Author by : Anonim
Languange : en
Publisher by : Academic Press
Format Available : PDF, ePub, Mobi
Total Read : 72
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Description : Computational Molecular modelling in Structural Biology, Volume 113, the latest release in the Advances in Protein Chemistry and Structural Biology, highlights new advances in the field, with this new volume presenting interesting chapters on charting the Bromodomain BRD4: Towards the Identification of Novel Inhibitors with Molecular Similarity and Receptor Mapping, and Computational Methods to Discover Compounds for the Treatment of Chagas Disease. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Advances in Protein Chemistry and Structural Biology series Updated, with the latest information on Computational Molecular Modelling in Structural Biology


Biophysical Chemistry

Author by : Anonim
Languange : en
Publisher by : BoD – Books on Demand
Format Available : PDF, ePub, Mobi
Total Read : 77
Total Download : 349
File Size : 54,5 Mb
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Description : Biophysical chemistry is one of the most interesting interdisciplinary research fields. Some of its different subjects have been intensively studied for decades. Now the field attracts not only scientists from chemistry, physics, and biology backgrounds but also those from medicine, pharmacy, and other sciences. We aimed to start this version of the book Biophysical Chemistry from advanced principles, as we include some of the most advanced subject matter, such as advanced topics in catalysis applications (first section) and therapeutic applications (second section). This led us to limit our selection to only chapters with high standards, therefore there are only six chapters, divided into two sections. We have assumed that the interested readers are familiar with the fundamentals of some advanced topics in mathematics such as integration, differentiation, and calculus and have some knowledge of organic and physical chemistry, biology, and pharmacy. We hope that the book will be valuable to graduate and postdoctoral students with the requisite background, and by some advanced researchers active in chemistry, biology, biochemistry, medicine, pharmacy, and other sciences.


Structure Based Drug Design For Diagnosis And Treatment Of Neurological Diseases

Author by : Rona R. Ramsay
Languange : en
Publisher by : Frontiers Media SA
Format Available : PDF, ePub, Mobi
Total Read : 42
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Description : European Cooperation in Science and Technology (COST) supports the collaboration of nationally-funded science and technology research through the creation of networks. COST is the longest-running European framework enhancing cooperation among researchers, engineers and scholars across Europe. The COST Action CM1103 “Structure-based drug design for diagnosis and treatment of neurological diseases: dissecting and modulating complex function in the monoaminergic systems of the brain” is a good example of the advances possible through interdisciplinary collaboration on difficult problems. COST Action CM1103 brought together 28 research groups from 18 countries to collaborate for four years on multi-target drug design for complex neuropathologies. The interdisciplinary expertise of the members is spans the range from computational enzymology to human studies, providing outstanding opportunities for the interdisciplinary development of trainees, and is reflected in the articles in this e-book. This Research Topic covers progress in multi-target drug design for the complex neuropathologies of the monoamine system that are apparent, for example, in Alzheimer’s disease. After a mini-review to introduce the topic of multi-target drug design, the other articles review the Research topic from their own perspective, two from computational approaches, three from medicinal chemistry, two from molecular pharmacology, and two from studies in whole brain. This multi-faceted approach describes new compounds, new methodology, and advances in the basic science of understanding the brain. This Ebook is based upon work from COST Action (CM1103 “Structure-based drug design for diagnosis and treatment of neurological diseases: dissecting and modulating complex function in the monoaminergic systems of the brain"), supported by COST (European Cooperation in Science and Technology). COST (European Cooperation in Science and Technology) is a pan-European intergovernmental framework. Its mission is to enable break-through scientific and technological developments leading to new concepts and products and thereby contribute to strengthening Europe’s research and innovation capacities. It allows researchers, engineers and scholars to jointly develop their own ideas and take new initiatives across all fields of science and technology, while promoting multi- and interdisciplinary approaches. COST aims at fostering a better integration of less research intensive countries to the knowledge hubs of the European Research Area. The COST Association, an International not-for-profit Association under Belgian Law, integrates all management, governing and administrative functions necessary for the operation of the framework. The COST Association has currently 36 Member Countries. www.cost.eu


Computational Approaches For Studying Enzyme Mechanism

Author by : Anonim
Languange : en
Publisher by : Academic Press
Format Available : PDF, ePub, Mobi
Total Read : 25
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Description : Computational Approaches for Studying Enzyme Mechanism Part A, is the first of two volumes in the Methods in Enzymology series, focusses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, and genetics to name a few. Focuses on computational approaches for studying enzyme mechanism Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods in intermediate filament associated proteins, and contains sections on such topics as lamin-associated proteins, intermediate filament-associated proteins and plakin, and other cytoskeletal cross-linkers


Variational Methods In Molecular Modeling

Author by : Jianzhong Wu
Languange : en
Publisher by : Springer
Format Available : PDF, ePub, Mobi
Total Read : 95
Total Download : 512
File Size : 43,5 Mb
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Description : This book presents tutorial overviews for many applications of variational methods to molecular modeling. Topics discussed include the Gibbs-Bogoliubov-Feynman variational principle, square-gradient models, classical density functional theories, self-consistent-field theories, phase-field methods, Ginzburg-Landau and Helfrich-type phenomenological models, dynamical density functional theory, and variational Monte Carlo methods. Illustrative examples are given to facilitate understanding of the basic concepts and quantitative prediction of the properties and rich behavior of diverse many-body systems ranging from inhomogeneous fluids, electrolytes and ionic liquids in micropores, colloidal dispersions, liquid crystals, polymer blends, lipid membranes, microemulsions, magnetic materials and high-temperature superconductors. All chapters are written by leading experts in the field and illustrated with tutorial examples for their practical applications to specific subjects. With emphasis placed on physical understanding rather than on rigorous mathematical derivations, the content is accessible to graduate students and researchers in the broad areas of materials science and engineering, chemistry, chemical and biomolecular engineering, applied mathematics, condensed-matter physics, without specific training in theoretical physics or calculus of variations.


Quantum Chemistry Simulation Of Biological Molecules

Author by : Eudenilson Albuquerque
Languange : en
Publisher by : Cambridge University Press
Format Available : PDF, ePub, Mobi
Total Read : 64
Total Download : 637
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Description : "Nano-biotechnology crosses the boundaries between physics, biochemistry and bioengineering, and has profound implications for the biomedical engineering industry. This book describes the quantum chemical simulation of a wide variety of molecular systems, with detailed analysis of their quantum chemical properties, individual molecular configurations, and cutting-edge biomedical applications. Topics covered include the basic properties of quantum chemistry and its conceptual foundations, the nanoelectronics and thermodynamics of DNA, the optoelectronic properties of the five DNA/RNA nucleobase anhydrous crystals, and key examples of molecular diode prototypes. A wide range of important applications are described, including protein binding of drugs such as cholesterol-lowering, anti- Parkinson and anti-migraine drugs, and recent developments in cancer biology are also discussed. This modern and comprehensive text is essential reading for graduate students and researchers in multidisciplinary areas of biological physics, chemical physics, chemical engineering, biochemistry and bioengineering"--


Kinetics And Dynamics

Author by : Piotr Paneth
Languange : en
Publisher by : Springer Science & Business Media
Format Available : PDF, ePub, Mobi
Total Read : 34
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Description : "Kinetics and Dynamics" on molecular modeling of dynamic processes opens with an introductory overview before discussing approaches to reactivity of small systems in the gas phase. Then it examines studies of systems of increasing complexity up to the dynamics of DNA. This title has interdisciplinary character presenting wherever possible an interplay between the theory and the experiment. It provides basic information as well as the details of theory and examples of its application to experimentalists and theoreticians interested in modeling of dynamic processes in chemical and biochemical systems. All contributing authors are renowned experts in their fields and topics covered in this volume represent the forefront of today’s science.


New Approaches For Flavin Catalysis

Author by : Anonim
Languange : en
Publisher by : Academic Press
Format Available : PDF, ePub, Mobi
Total Read : 32
Total Download : 279
File Size : 45,7 Mb
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Description : New Approaches for Flavin Catalysis, Volume 620, a new volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Topics covered in this update include Anaerobiosis and Methods for Reduction, Reduction Potentials, Anaerobic Stopped-Flow, No Glove-Box, Anaerobic Stopped-Flow, in a Glove-Box, Chemical Quenching, Oxygen Reactions, Double-mixing Stopped-Flow, Kinetic Isotope Effects and Viscosity Effects, Heavy Enzymes Synthetic Flavins & Linear Free Energy Relationships, Vibrational Spectroscopy, Stark Spectroscopy, EPR and Related Methods, Molecular Dynamics, Phylogenetic Relationships/Superfamilies, O2 and Superoxide Analogs, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology series Updated release includes the latest information on New Approaches for Flavin Catalysis


Iutam Symposium On Nonlinear Stochastic Dynamics And Control

Author by : W.Q. Zhu
Languange : en
Publisher by : Springer Science & Business Media
Format Available : PDF, ePub, Mobi
Total Read : 17
Total Download : 901
File Size : 49,8 Mb
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Description : Non-linear stochastic systems are at the center of many engineering disciplines and progress in theoretical research had led to a better understanding of non-linear phenomena. This book provides information on new fundamental results and their applications which are beginning to appear across the entire spectrum of mechanics. The outstanding points of these proceedings are Coherent compendium of the current state of modelling and analysis of non-linear stochastic systems from engineering, applied mathematics and physics point of view. Subject areas include: Multiscale phenomena, stability and bifurcations, control and estimation, computational methods and modelling. For the Engineering and Physics communities, this book will provide first-hand information on recent mathematical developments. The applied mathematics community will benefit from the modelling and information on various possible applications.


Virtual Drug Design

Author by : Daniela Schuster
Languange : en
Publisher by : Frontiers Media SA
Format Available : PDF, ePub, Mobi
Total Read : 57
Total Download : 544
File Size : 41,7 Mb
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Description : In the current drug research environment in academia and industry, cheminformatics and virtual screening methods are well established and integrated tools. Computational tools are used to predict a compound’s 3D structure, the 3D structure and function of a pharmacological target, ligand-target interactions, binding energies, and other factors essential for a successful drug. This includes molecular properties such as solubility, logP value, susceptibility to metabolism, cell permeation, blood brain barrier permeation, interaction with drug transporters and potential off-target effects. Given that approximately 40 million unique compounds are readily available for purchase, such computational modeling and filtering tools are essential to support the drug discovery and development process. The aim of all these calculations is to focus experimental efforts on the most promising candidates and exclude problematic compounds early in the project. In this Research Topic on virtual activity predictions, we cover several aspects of this research area such as historical perspectives, data sources, ligand treatment, virtual screening methods, hit list handling and filtering.


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

Author by : Adam Liwo
Languange : en
Publisher by : Springer Science & Business Media
Format Available : PDF, ePub, Mobi
Total Read : 63
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File Size : 55,8 Mb
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Description : Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.


Handbook Of Biochemical Kinetics

Author by : Daniel L. Purich
Languange : en
Publisher by : Elsevier
Format Available : PDF, ePub, Mobi
Total Read : 34
Total Download : 194
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Description : Biochemical kinetics refers to the rate at which a reaction takes place. Kinetic mechanisms have played a major role in defining the metabolic pathways, the mechanistic action of enzymes, and even the processing of genetic material. The Handbook of Biochemical Kinetics provides the "underlying scaffolding" of logic for kinetic approaches to distinguish rival models or mechanisms. The handbook also comments on techniques and their likely limitations and pitfalls, as well as derivations of fundamental rate equations that characterize biochemical processes. Key Features * Over 750 pages devoted to theory and techniques for studying enzymic and metabolic processes * Over 1,500 definitions of kinetic and mechanistic terminology, with key references * Practical advice on experimental design of kinetic experiments * Extended step-by-step methods for deriving rate equations * Over 1,000 enzymes, complete with EC numbers, reactions catalyzed, and references to reviews and/or assay methods * Over 5,000 selected references to kinetic methods appearing in the Methods in Enzymology series * 72-page Wordfinder that allows the reader to search by keywords * Summaries of mechanistic studies on key enzymes and protein systems * Over 250 diagrams, figures, tables, and structures


The Scale Of Nature

Author by : John Tyler Bonner
Languange : en
Publisher by : Unknown
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Quantitative Understanding Of Biosystems

Author by : Thomas M. Nordlund
Languange : en
Publisher by : CRC Press
Format Available : PDF, ePub, Mobi
Total Read : 52
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File Size : 42,8 Mb
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Description : Quantitative Understanding of Biosystems: An Introduction to Biophysics focuses on the behavior and properties of microscopic structures that underlie living systems. It clearly describes the biological physics of macromolecules, subcellular structures, and whole cells, including interactions with light. Providing broad coverage of physics, chemistry, biology, and mathematics, this color text features: Mathematical and computational tools—graphing, calculus, simple differential equations, diagrammatic analysis, and visualization tools Randomness, variation, statistical mechanics, distributions, and spectra The biological micro- and nanoworld—structures, processes, and the physical laws Quantum effects—photosynthesis, UV damage, electron and energy transfer, and spectroscopic characterization of biological structures Through its active learning approach, the text encourages practical comprehension of the behavior of biosystems, rather than knowledge of the latest research. The author includes graph- and diagram-centered physics and mathematics, simple software, frequent checks of understanding, and a repetition of important ideas at higher levels or from different points of view. After completing this book, students will gain significant computational and project experience and become competent at quantitatively characterizing biosystems. CD-ROM Resource The accompanying CD contains multimedia learning tools, such as video clips and animations, that illustrate intrinsically dynamic processes. For students inexperienced in the application of mathematics and physical principles to naturally occurring phenomena, this multimedia component emphasizes what is most obvious about biological systems: living things move. Students can also manipulate and re-program the included Excel graphs.


Handbook Of Computational Chemistry

Author by : Jerzy Leszczynski
Languange : en
Publisher by : Springer Science & Business Media
Format Available : PDF, ePub, Mobi
Total Read : 91
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File Size : 52,7 Mb
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Description : This handbook is a guide to current methods of computational chemistry, explaining their limitations and advantages and providing examples of their applications. The first part outlines methods, the balance of volumes present numerous important applications.


Current Research In Britain

Author by : Anonim
Languange : en
Publisher by : Unknown
Format Available : PDF, ePub, Mobi
Total Read : 61
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Science

Author by : John Michels
Languange : en
Publisher by : Unknown
Format Available : PDF, ePub, Mobi
Total Read : 67
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Description : A weekly record of scientific progress.


Computational Methods For Understanding Riboswitches

Author by : Anonim
Languange : en
Publisher by : Academic Press
Format Available : PDF, ePub, Mobi
Total Read : 39
Total Download : 323
File Size : 41,5 Mb
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Description : This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers computational prediction RNA structure and dynamics, including such topics as computational modeling of RNA secondary and tertiary structures, riboswitch dynamics, and ion-RNA, ligand-RNA and DNA-RNA interactions. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers computational methods and applications in RNA structure and dynamics Contains chapters with emerging topics such as RNA structure prediction, riboswitch dynamics and thermodynamics, and effects of ions and ligands.


Epa Publications Bibliography

Author by : Anonim
Languange : en
Publisher by : Unknown
Format Available : PDF, ePub, Mobi
Total Read : 73
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Conference Papers Index

Author by : Anonim
Languange : en
Publisher by : Unknown
Format Available : PDF, ePub, Mobi
Total Read : 53
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Description : Monthly. Papers presented at recent meeting held all over the world by scientific, technical, engineering and medical groups. Sources are meeting programs and abstract publications, as well as questionnaires. Arranged under 17 subject sections, 7 of direct interest to the life scientist. Full programs of meetings listed under sections. Entry gives citation number, paper title, name, mailing address, and any ordering number assigned. Quarterly and annual indexes to subjects, authors, and programs (not available in monthly issues).


Louisiana Agriculture

Author by : Anonim
Languange : en
Publisher by : Unknown
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Total Read : 45
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Description :


Catalogs Of Courses

Author by : University of California, Berkeley
Languange : en
Publisher by : Unknown
Format Available : PDF, ePub, Mobi
Total Read : 84
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Description : Includes general and summer catalogs issued between 1878/1879 and 1995/1997.