Prediction Of Protein Structure And The Principles Of Protein Conformation
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Prediction Of Protein Structure And The Principles Of Protein Conformation
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Author : G.D. Fasman
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-12-06
Prediction Of Protein Structure And The Principles Of Protein Conformation written by G.D. Fasman and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-12-06 with Science categories.
The prediction of the conformation of proteins has developed from an intellectual exercise into a serious practical endeavor that has great promise to yield new stable enzymes, products of pharmacological significance, and catalysts of great potential. With the application of predic tion gaining momentum in various fields, such as enzymology and immunology, it was deemed time that a volume be published to make available a thorough evaluation of present methods, for researchers in this field to expound fully the virtues of various algorithms, to open the field to a wider audience, and to offer the scientific public an opportunity to examine carefully its successes and failures. In this manner the practitioners of the art could better evaluate the tools and the output so that their expectations and applications could be more realistic. The editor has assembled chapters by many of the main contributors to this area and simultaneously placed their programs at three national resources so that they are readily available to those who wish to apply them to their personal interests. These algorithms, written by their originators, when utilized on pes or larger computers, can instantaneously take a primary amino acid sequence and produce a two-or three-dimensional artistic image that gives satisfaction to one's esthetic sensibilities and food for thought concerning the structure and function of proteins. It is in this spirit that this volume was envisaged.
The Protein Folding Problem And Tertiary Structure Prediction
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Author : Kenneth M.Jr. Merz
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-12-06
The Protein Folding Problem And Tertiary Structure Prediction written by Kenneth M.Jr. Merz and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-12-06 with Medical categories.
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.
Protein Folding In Silico
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Author : Irena Roterman-Konieczna
language : en
Publisher: Elsevier
Release Date : 2012-10-04
Protein Folding In Silico written by Irena Roterman-Konieczna and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-10-04 with Science categories.
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
Protein Structure Prediction
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Author : Michael J. E. Sternberg
language : en
Publisher: Oxford University Press on Demand
Release Date : 1996
Protein Structure Prediction written by Michael J. E. Sternberg and has been published by Oxford University Press on Demand this book supported file pdf, txt, epub, kindle and other format this book has been release on 1996 with Philosophy categories.
The three-dimensional structure of proteins is a key factor in their biological activity. There is an increasing need to be able to predict the structure of a protein once its amino-acid sequence is known; this book presents practical methods of achieving that ambitious aim, using the latest computer modelling algorithms.
Protein Structure
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Author : Harold A. Scheraga
language : en
Publisher: Academic Press
Release Date : 2014-07-01
Protein Structure written by Harold A. Scheraga and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-07-01 with Technology & Engineering categories.
Protein Structure deals with the chemistry and physics of biologically important molecules—the proteins—particularly the determination of the structure of various proteins, their thermodynamics, their kinetics, and the mechanisms of different reactions of individual proteins. The book approaches the study of protein structure in two ways: firstly, by determining the general features of protein structure, the overall size, and shape of the molecule; and secondly, by investigating the molecule internally along with the various aspects of the internal configuration of protein molecules. It describes in detail experimental methods for determining protein structure in solution, such as the hydrodynamic method, the thermodynamic optical method, and the electrochemical method. The book then explains the results of experiments carried out on insulin, lysozyme, and ribonuclease. The text notes that the experiments, carried out on native and denatured proteins as well as on derivatives prepared by chemical modification (e.g., by methylation, iodination, acetylation, etc.), can lead to greater understanding of secondary and tertiary structures of proteins of known sequence. The book is suitable for biochemists, micro-biologists, cellular researchers, or investigators involved in protein structure and other biological sciences related to muscle physiologists, geneticists, enzymologists, or immunologists.
Homology Molecular Modeling
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Author : Rafael Trindade Maia
language : en
Publisher: BoD – Books on Demand
Release Date : 2021-03-10
Homology Molecular Modeling written by Rafael Trindade Maia and has been published by BoD – Books on Demand this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-03-10 with Science categories.
Homology modeling is an extremely useful and versatile technique that is gaining more and more space and demand in research in computational and theoretical biology. This book, “Homology Molecular Modeling - Perspectives and Applications”, brings together unpublished chapters on this technique. In this book, 7 chapters are intimately related to the theme of molecular modeling, carefully selected and edited for academic and scientific readers. It is an indispensable read for anyone interested in the areas of bioinformatics and computational biology. Divided into 4 sections, the reader will have a didactic and comprehensive view of the theme, with updated and relevant concepts on the subject. This book was organized from researchers to researchers with the aim of spreading the fascinating area of molecular modeling by homology.
The Physical Foundation Of Protein Architecture
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Author : Nobuhiko Saito
language : en
Publisher: World Scientific
Release Date : 2001
The Physical Foundation Of Protein Architecture written by Nobuhiko Saito and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2001 with Science categories.
A protein requires its own three-dimensional structure for its biological activity. If a chemical agent is added, the biological activity is lost, and the three dimensional structure is destroyed to become a random coil state. But when the chemical agent is removed, the biological activity is recovered, implying that the random coil state turns back into the original complex structure spontaneously. This is an astonishing event. The Physical Foundation of Protein Architecture is intended to solve this mystery from the physicochemical basis by elucidating the mechanism of various processes in protein folding. The main features of protein folding are shown to be described by the island model with long range hydrophobic interaction which is capable of finding the specific residue, and the lampshade criterion for disulfide bonding. Various proteins with known structure are refolded, with the purpose of uncovering the mechanism of protein folding. In addition, ab initio method for predicting protein structure from its amino acid sequence is proposed.
Principles Of Protein Structure
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Author : Ivet Bahar
language : en
Publisher: Garland Science
Release Date : 2017-02-09
Principles Of Protein Structure written by Ivet Bahar and has been published by Garland Science this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-02-09 with Science categories.
Protein Actions: Principles and Modeling is aimed at graduates, advanced undergraduates, and any professional who seeks an introduction to the biological, chemical, and physical properties of proteins. Broadly accessible to biophysicists and biochemists, it will be particularly useful to student and professional structural biologists and molecular biophysicists, bioinformaticians and computational biologists, biological chemists (particularly drug designers) and molecular bioengineers. The book begins by introducing the basic principles of protein structure and function. Some readers will be familiar with aspects of this, but the authors build up a more quantitative approach than their competitors. Emphasizing concepts and theory rather than experimental techniques, the book shows how proteins can be analyzed using the disciplines of elementary statistical mechanics, energetics, and kinetics. These chapters illuminate how proteins attain biologically active states and the properties of those states. The book ends with a synopsis the roles of computational biology and bioinformatics in protein science.
Prediction Of Protein Secondary Structure
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Author : Andrzej Kloczkowski
language : en
Publisher: Springer Nature
Release Date : 2024-11-22
Prediction Of Protein Secondary Structure written by Andrzej Kloczkowski and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-11-22 with Science categories.
This second edition volume expands on the previous edition with updates on the latest methods, resources, and studies concerning analysis and prediction of various structural and functional aspects of proteins and ncRNAs. The chapters in this book cover topics such as secondary structure characterization and prediction; the use and impact of AI (including AlphaFold, large language models, and deep neural networks) in the protein structure prediction field; methods and resources for the prediction of posttranslational modifications, residue-residue contacts, subcellular localization, intrinsic disorder, protein-ligand interactions, and protein aggregation; analysis of cryo-EM data; and analysis of noncoding RNAs in the context of human diseases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions and surveys of the respective topics, list the necessary materials and methods, cover step-by-step instructions on how to use predictive tools and interpret their results, and provide tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Prediction of Protein Secondary Structure, Second Edition is a valuable resource for anyone interested in understanding the dynamic and growing field of the protein structure prediction.
Protein Protein Interaction Regulators
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Author : Siddhartha Roy
language : en
Publisher: Royal Society of Chemistry
Release Date : 2020-12-15
Protein Protein Interaction Regulators written by Siddhartha Roy and has been published by Royal Society of Chemistry this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-12-15 with Science categories.
New genomic information has revealed the crucial role that protein-protein interactions (PPIs) play in regulating numerous cellular functions. Aberrant forms of these interactions are common in numerous diseases and thus PPIs have emerged as a vast class of critical drug targets. Despite the importance of PPIs in biology, it has been extremely challenging to convert targets into therapeutics and targeting PPIs had long been considered a very difficult task. However, over the past decade the field has advanced with increasing growth in the number of successful PPI regulators. Protein-Protein Interaction Regulators surveys the latest advances in the structural understanding of PPIs as well as recent developments in modulator discovery.