The Protein Folding Problem

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The Protein Folding Problem and Tertiary Structure Prediction

Author : Kenneth M.Jr. Merz
Publisher : Springer Science & Business Media
ISBN 13 : 1468468316
Total Pages : 585 pages
Book Rating : 4.4/5 (684 download)

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Book Synopsis The Protein Folding Problem and Tertiary Structure Prediction by : Kenneth M.Jr. Merz

Download or read book The Protein Folding Problem and Tertiary Structure Prediction written by Kenneth M.Jr. Merz and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 585 pages. Available in PDF, EPUB and Kindle. Book excerpt: A solution to the protein folding problem has eluded researchers for more than 30 years. The stakes are high. Such a solution will make 40,000 more tertiary structures available for immediate study by translating the DNA sequence information in the sequence databases into three-dimensional protein structures. This translation will be indispensable for the analy sis of results from the Human Genome Project, de novo protein design, and many other areas of biotechnological research. Finally, an in-depth study of the rules of protein folding should provide vital clues to the protein fold ing process. The search for these rules is therefore an important objective for theoretical molecular biology. Both experimental and theoretical ap proaches have been used in the search for a solution, with many promising results but no general solution. In recent years, there has been an exponen tial increase in the power of computers. This has triggered an incredible outburst of theoretical approaches to solving the protein folding problem ranging from molecular dynamics-based studies of proteins in solution to the actual prediction of protein structures from first principles. This volume attempts to present a concise overview of these advances. Adrian Roitberg and Ron Elber describe the locally enhanced sam pling/simulated annealing conformational search algorithm (Chapter 1), which is potentially useful for the rapid conformational search of larger molecular systems.

The Protein Folding Problem and Its Solutions

Author : Arieh Ben-Naim
Publisher : World Scientific Publishing Company Incorporated
ISBN 13 : 9789814436359
Total Pages : 297 pages
Book Rating : 4.4/5 (363 download)

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Book Synopsis The Protein Folding Problem and Its Solutions by : Arieh Ben-Naim

Download or read book The Protein Folding Problem and Its Solutions written by Arieh Ben-Naim and published by World Scientific Publishing Company Incorporated. This book was released on 2013 with total page 297 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a new approach to the Protein Folding Problem. It starts with a clear description of what the protein folding problem involves. Then, it suggests non-conventional answers to some of the questions posed. In particular, it emphasizes the importance of hydrophilic interactions and hydrophilic forces, rather than the hydrophobic effects, for the stability of the native structure of proteins, as well for the speed of the folding process.

Protein Simulations

Author : Valerie Daggett
Publisher : Elsevier
ISBN 13 : 0080493785
Total Pages : 477 pages
Book Rating : 4.0/5 (84 download)

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Book Synopsis Protein Simulations by : Valerie Daggett

Download or read book Protein Simulations written by Valerie Daggett and published by Elsevier. This book was released on 2003-11-26 with total page 477 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein 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

Protein Stability and Folding

Author : Wolfgang Pfeil
Publisher : Springer Science & Business Media
ISBN 13 : 3642587607
Total Pages : 662 pages
Book Rating : 4.6/5 (425 download)

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Book Synopsis Protein Stability and Folding by : Wolfgang Pfeil

Download or read book Protein Stability and Folding written by Wolfgang Pfeil and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 662 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding remains one of the most exclusive problems of modern biochemistry. Structure analysis has given access to the wealth of the molecular architecture of pro teins. As architecture needs static calculations, protein structure is always related to thermodynamic factors that govern folding and stability of a particular folded protein over the non-organized polypeptide chain. During the past decades a huge amount of thermodynamic data related to protein folding and stability has been accumulated. The data are certainly of importance in dechiffring the protein folding problem. At the same time, the data can guide the con struction of modified and newly synthesized proteins with properties optimized for particular application. The intention of this book is a generation of a data collection which makes the vast amount of present data accessible for multidisciplinary research where chemistry, phy sics, biology, and medicine are involved and also pharmaceutical and food research and technology. It took several years to compile all the data and the author wishes to thank everyone who provided data, ideas or even unpublished results. The author is, in particular, indebted to Prof. Wadso (Lund, Sweden) and IUPAC's Steering Committee on Bio physical Chemistry. Furthermore, support by the Deutsche Forschungsgemeinschafi (INK 16 AI-I) is acknowledged.

The Protein Folding Problem

Author : Donald B Wetlaufer
Publisher : Routledge
ISBN 13 : 9780367310851
Total Pages : 0 pages
Book Rating : 4.3/5 (18 download)

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Book Synopsis The Protein Folding Problem by : Donald B Wetlaufer

Download or read book The Protein Folding Problem written by Donald B Wetlaufer and published by Routledge. This book was released on 2024-10-31 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book introduces the central problem of folding mechanisms as well as a number of other closely related issues. This book is neither a textbook nor a treatise. Rather, it is an attempt by several investigators to convey the excitement and challenges of those aspects of the folding problem in which they are actively engaged.

Protein Physics

Author : Alexei V. Finkelstein
Publisher : Elsevier
ISBN 13 : 0081012365
Total Pages : 530 pages
Book Rating : 4.0/5 (81 download)

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Book Synopsis Protein Physics by : Alexei V. Finkelstein

Download or read book Protein Physics written by Alexei V. Finkelstein and published by Elsevier. This book was released on 2016-06-22 with total page 530 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Physics: A Course of Lectures covers the most general problems of protein structure, folding and function. It describes key experimental facts and introduces concepts and theories, dealing with fibrous, membrane, and water-soluble globular proteins, in both their native and denatured states. The book systematically summarizes and presents the results of several decades of worldwide fundamental research on protein physics, structure, and folding, describing many physical models that help readers make estimates and predictions of physical processes that occur in proteins. New to this revised edition is the inclusion of novel information on amyloid aggregation, natively disordered proteins, protein folding in vivo, protein motors, misfolding, chameleon proteins, advances in protein engineering & design, and advances in the modeling of protein folding. Further, the book provides problems with solutions, many new and updated references, and physical and mathematical appendices. In addition, new figures (including stereo drawings, with a special appendix showing how to use them) are added, making this an ideal resource for graduate and advanced undergraduate students and researchers in academia in the fields of biophysics, physics, biochemistry, biologists, biotechnology, and chemistry. - Fully revised and expanded new edition based on the latest research developments in protein physics - Written by the world's top expert in the field - Deals with fibrous, membrane, and water-soluble globular proteins, in both their native and denatured states - Summarizes, in a systematic form, the results of several decades of worldwide fundamental research on protein physics and their structure and folding - Examines experimental data on protein structure in the post-genome era

Protein Folding in Silico

Author : Irena Roterman-Konieczna
Publisher : Elsevier
ISBN 13 : 1908818255
Total Pages : 241 pages
Book Rating : 4.9/5 (88 download)

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Book Synopsis Protein Folding in Silico by : Irena Roterman-Konieczna

Download or read book Protein Folding in Silico written by Irena Roterman-Konieczna and published by Elsevier. This book was released on 2012-10-04 with total page 241 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding is a process by which a protein structure assumes its functional shape of conformation, and has been the subject of research since the publication of the first software tool for protein structure prediction. Protein folding in silico approaches this issue by introducing an ab initio model that attempts to simulate as far as possible the folding process as it takes place in vivo, and attempts to construct a mechanistic model on the basis of the predictions made. The opening chapters discuss the early stage intermediate and late stage intermediate models, followed by a discussion of structural information that affects the interpretation of the folding process. The second half of the book covers a variety of topics including ligand binding site recognition, the "fuzzy oil drop" model and its use in simulation of the polypeptide chain, and misfolded proteins. The book ends with an overview of a number of other ab initio methods for protein structure predictions and some concluding remarks. - Discusses a range of ab initio models for protein structure prediction - Introduces a unique model based on experimental observations - Describes various methods for the quantitative assessment of the presented models from the viewpoint of information theory

Free Energy Calculations

Author : Christophe Chipot
Publisher : Springer Science & Business Media
ISBN 13 : 3540384472
Total Pages : 528 pages
Book Rating : 4.5/5 (43 download)

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Book Synopsis Free Energy Calculations by : Christophe Chipot

Download or read book Free Energy Calculations written by Christophe Chipot and published by Springer Science & Business Media. This book was released on 2007-01-08 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Free 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.

Protein Folding

Author : Charis Ghélis
Publisher :
ISBN 13 :
Total Pages : 592 pages
Book Rating : 4.:/5 (319 download)

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Book Synopsis Protein Folding by : Charis Ghélis

Download or read book Protein Folding written by Charis Ghélis and published by . This book was released on 1982 with total page 592 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Folding aims to collect the most important information in the field of protein folding and probes the main principles that govern formation of the three-dimensional structure of a protein from a nascent polypeptide chain, as well as how the functional properties appear. This text is organized into three sections and consists of 15 chapters. After an introductory chapter where the main problems of protein folding are considered at the cellular level in the context of protein biosynthesis, the discussion turns to the conformation of native globular proteins. Definitions and rules of nome ...

Mechanisms of Protein Folding

Author : Roger H. Pain
Publisher : Oxford University Press, USA
ISBN 13 : 9780199637881
Total Pages : 433 pages
Book Rating : 4.6/5 (378 download)

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Book Synopsis Mechanisms of Protein Folding by : Roger H. Pain

Download or read book Mechanisms of Protein Folding written by Roger H. Pain and published by Oxford University Press, USA. This book was released on 2000 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the publication of the first edition of mechanisms of protein folding in 1994, significant advances in both the technical and conceptual understanding of protein folding. This new edition has been brought up to date in content, context, and authorship and will make the subject accessibleto a wide range of scientists. The emphasis on experimental approaches has benn maintained from the first edition but this time within the explicit context of simulations and energy surfaces. There is an introductory chapter explaining the 'new' model of protein folding, which takes into account theheterogeneity of the starting state. Advances in interpreting observed kinetic data and the development of technology to observe fast folding reactions and characterize intermediate structures have accompanied this new view and are covered in detail. The term 'molten globule'is often usedincorrectly but here the significance of the term is carefully described at different satges of folding. The concept of the transition state, including the complementary approaches of molecular dynamics and protein engineering, is also discussed in detail. In vitro studies provide the molecularbasis for the thermodynamic and kinetic energy minimization of the in vivo processes of protein folding and two of the potentially rate determining reactions are disulphide bond formation and proline isomerization. It has also become increasingly apparent that chaperone proteins play a vital role inprotein folding and other reactions of proteins involoving major conformational change and the molecular details of these processes are discussed in detail in chapter 14. The final chapter describes the centreal importance of protein folding and unfolding reactions in disease and gives claerdefinition of the term 'misfolding'. Studying protein folding in vivo is full of problems and to show how these problems can be overcome in practice, three case studies of three very different types of protein have been included: the small globular protein apomyoglobin; the fibrous protein collagen;and the membrane protein haemagglutinin.

Oxidative Folding of Peptides and Proteins

Author : Luis Moroder
Publisher : Royal Society of Chemistry
ISBN 13 : 0854041486
Total Pages : 453 pages
Book Rating : 4.8/5 (54 download)

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Book Synopsis Oxidative Folding of Peptides and Proteins by : Luis Moroder

Download or read book Oxidative Folding of Peptides and Proteins written by Luis Moroder and published by Royal Society of Chemistry. This book was released on 2009 with total page 453 pages. Available in PDF, EPUB and Kindle. Book excerpt: With contributions from experts in the field, this book provides a comprehensive overview of the oxidative folding of cysteine-rich peptides.

Fuzzy Logic Augmentation of Neural and Optimization Algorithms: Theoretical Aspects and Real Applications

Author : Oscar Castillo
Publisher : Springer
ISBN 13 : 3319710087
Total Pages : 535 pages
Book Rating : 4.3/5 (197 download)

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Book Synopsis Fuzzy Logic Augmentation of Neural and Optimization Algorithms: Theoretical Aspects and Real Applications by : Oscar Castillo

Download or read book Fuzzy Logic Augmentation of Neural and Optimization Algorithms: Theoretical Aspects and Real Applications written by Oscar Castillo and published by Springer. This book was released on 2018-01-10 with total page 535 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book comprises papers on diverse aspects of fuzzy logic, neural networks, and nature-inspired optimization meta-heuristics and their application in various areas such as intelligent control and robotics, pattern recognition, medical diagnosis, time series prediction and optimization of complex problems. The book is organized into seven main parts, each with a collection of papers on a similar subject. The first part presents new concepts and algorithms based on type-2 fuzzy logic for dynamic parameter adaptation in meta-heuristics. The second part discusses network theory and applications, and includes papers describing applications of neural networks in diverse areas, such as time series prediction and pattern recognition. The third part addresses the theory and practice of meta-heuristics in different areas of application, while the fourth part describes diverse fuzzy logic applications in the control area, which can be considered as intelligent controllers. The next two parts explore applications in areas, such as time series prediction, and pattern recognition and new optimization and evolutionary algorithms and their applications respectively. Lastly, the seventh part addresses the design and application of different hybrid intelligent systems.

The State of Science

Author : Marc Zimmer
Publisher : Rowman & Littlefield
ISBN 13 : 1633886409
Total Pages : 221 pages
Book Rating : 4.6/5 (338 download)

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Book Synopsis The State of Science by : Marc Zimmer

Download or read book The State of Science written by Marc Zimmer and published by Rowman & Littlefield. This book was released on 2020-07-20 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: New research and innovations in the field of science are leading to life-changing and world-altering discoveries like never before. What does the horizon of science look like? Who are the scientists that are making it happen? And, how are we to introduce these revolutions to a society in which a segment of the population has become more and more skeptical of science? Climate change is the biggest challenge facing our nation, and scientists are working on renewable energy sources, meat alternatives, and carbon dioxide sequestration. At the same time, climate change deniers and the politicization of funding threaten their work. CRISPR, (Clustered Regularly Interspaced Short Palindromic Repeats) repurposes bacterial defense systems to edit genes, which can change the way we live, but also presents real ethical problems. Optogenetics will help neuroscientists map complicated neural circuitry deep inside the brain, shedding light on treating Alzheimer’s and Parkinson’s disease. Zimmer also investigates phony science ranging from questionable “health” products to the fervent anti-vaccination movement. Zimmer introduces readers to the real people making these breakthroughs. Concluding with chapters on the rise of women in STEM fields, the importance of US immigration policies to science, and new, unorthodox ways of DIY science and crowdsource funding, The State of Science shows where science is, where it is heading, and the scientists who are at the forefront of progress.

Fundamentals of Protein Structure and Function

Author : Engelbert Buxbaum
Publisher : Springer
ISBN 13 : 331919920X
Total Pages : 521 pages
Book Rating : 4.3/5 (191 download)

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Book Synopsis Fundamentals of Protein Structure and Function by : Engelbert Buxbaum

Download or read book Fundamentals of Protein Structure and Function written by Engelbert Buxbaum and published by Springer. This book was released on 2015-11-27 with total page 521 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book serves as an introduction to protein structure and function. Starting with their makeup from simple building blocks, called amino acids, the 3-dimensional structure of proteins is explained. This leads to a discussion how misfolding of proteins causes diseases like cancer, various encephalopathies, or diabetes. Enzymology and modern concepts of enzyme kinetics are then introduced, taking into account the physiological, pharmacological and medical significance of this often neglected topic. This is followed by thorough coverage of hæmoglobin and myoglobin, immunoproteins, motor proteins and movement, cell-cell interactions, molecular chaperones and chaperonins, transport of proteins to various cell compartments and solute transport across biological membranes. Proteins in the laboratory are also covered, including a detailed description of the purification and determination of proteins, as well as their characterisation for size and shape, structure and molecular interactions. The book emphasises the link between protein structure, physiological function and medical significance. This book can be used for graduate and advanced undergraduate classes covering protein structure and function and as an introductory text for researchers in protein biochemistry, molecular and cell biology, chemistry, biophysics, biomedicine and related courses. About the author: Dr. Buxbaum is a biochemist with interest in enzymology and protein science. He has been working on the biochemistry of membrane transport proteins for nearly thirty years and has taught courses in biochemistry and biomedicine at several universities.

Lectures On Statistical Physics And Protein Folding

Author : Kerson Huang
Publisher : World Scientific
ISBN 13 : 9814481068
Total Pages : 159 pages
Book Rating : 4.8/5 (144 download)

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Book Synopsis Lectures On Statistical Physics And Protein Folding by : Kerson Huang

Download or read book Lectures On Statistical Physics And Protein Folding written by Kerson Huang and published by World Scientific. This book was released on 2005-05-30 with total page 159 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book introduces an approach to protein folding from the point of view of kinetic theory. There is an abundance of data on protein folding, but few proposals are available on the mechanism driving the process. Here, presented for the first time, are suggestions on possible research directions, as developed by the author in collaboration with C C Lin.The first half of this invaluable book contains a concise but relatively complete review of relevant topics in statistical mechanics and kinetic theory. It includes standard topics such as thermodynamics, the Maxwell-Boltzmann distribution, and ensemble theory. Special discussions include the dynamics of phase transitions, and Brownian motion as an illustration of stochastic processes.The second half develops topics in molecular biology and protein structure, with a view to discovering mechanisms underlying protein folding. Attention is focused on the energy flow through the protein in its folded state. A mathematical model, based on the Brownian motion of coupled harmonic oscillators, is worked out in the appendix.

Protein Folding

Author : Thomas E. Creighton
Publisher : W. H. Freeman
ISBN 13 : 9780716770275
Total Pages : 547 pages
Book Rating : 4.7/5 (72 download)

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Book Synopsis Protein Folding by : Thomas E. Creighton

Download or read book Protein Folding written by Thomas E. Creighton and published by W. H. Freeman. This book was released on 1992-06-15 with total page 547 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Protein Folding and Metal Ions

Author : Cláudio M. Gomes
Publisher : CRC Press
ISBN 13 : 1439809658
Total Pages : 302 pages
Book Rating : 4.4/5 (398 download)

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Book Synopsis Protein Folding and Metal Ions by : Cláudio M. Gomes

Download or read book Protein Folding and Metal Ions written by Cláudio M. Gomes and published by CRC Press. This book was released on 2016-04-19 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: The role of metal ions in protein folding and structure is a critical topic to a range of scientists in numerous fields, particularly those working in structural biology and bioinorganic chemistry, those studying protein folding and disease, and those involved in the molecular and cellular aspects of metals in biological systems. Protein Folding an