Protein Structure Prediction
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Introduction To Protein Structure Prediction
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Author : Huzefa Rangwala
language : en
Publisher: John Wiley & Sons
Release Date : 2011-03-16
Introduction To Protein Structure Prediction written by Huzefa Rangwala and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-03-16 with Science categories.
A look at the methods and algorithms used to predict protein structure A thorough knowledge of the function and structure of proteins is critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this reference sheds light on the methods used for protein structure prediction and reveals the key applications of modeled structures. This indispensable book covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. With this resource, readers will find an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction and they will acquire unique insight into the future applications of the modeled protein structures. The book begins with a thorough introduction to the protein structure prediction problem and is divided into four themes: a background on structure prediction, the prediction of structural elements, tertiary structure prediction, and functional insights. Within those four sections, the following topics are covered: Databases and resources that are commonly used for protein structure prediction The structure prediction flagship assessment (CASP) and the protein structure initiative (PSI) Definitions of recurring substructures and the computational approaches used for solving sequence problems Difficulties with contact map prediction and how sophisticated machine learning methods can solve those problems Structure prediction methods that rely on homology modeling, threading, and fragment assembly Hybrid methods that achieve high-resolution protein structures Parts of the protein structure that may be conserved and used to interact with other biomolecules How the loop prediction problem can be used for refinement of the modeled structures The computational model that detects the differences between protein structure and its modeled mutant Whether working in the field of bioinformatics or molecular biology research or taking courses in protein modeling, readers will find the content in this book invaluable.
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.
From Protein Structure To Function With Bioinformatics
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Author : Daniel John Rigden
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-12-11
From Protein Structure To Function With Bioinformatics written by Daniel John Rigden 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 2008-12-11 with Science categories.
Proteins lie at the heart of almost all biological processes and have an incredibly wide range of activities. Central to the function of all proteins is their ability to adopt, stably or sometimes transiently, structures that allow for interaction with other molecules. An understanding of the structure of a protein can therefore lead us to a much improved picture of its molecular function. This realisation has been a prime motivation of recent Structural Genomics projects, involving large-scale experimental determination of protein structures, often those of proteins about which little is known of function. These initiatives have, in turn, stimulated the massive development of novel methods for prediction of protein function from structure. Since model structures may also take advantage of new function prediction algorithms, the first part of the book deals with the various ways in which protein structures may be predicted or inferred, including specific treatment of membrane and intrinsically disordered proteins. A detailed consideration of current structure-based function prediction methodologies forms the second part of this book, which concludes with two chapters, focusing specifically on case studies, designed to illustrate the real-world application of these methods. With bang up-to-date texts from world experts, and abundant links to publicly available resources, this book will be invaluable to anyone who studies proteins and the endlessly fascinating relationship between their structure and function.
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.
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.
Computational Methods For Protein Structure Prediction And Modeling
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Author : Ying Xu
language : en
Publisher: Springer
Release Date : 2010-11-29
Computational Methods For Protein Structure Prediction And Modeling written by Ying Xu and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-11-29 with Science categories.
Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information. Eleven chapters survey of the field, covering key topics in modeling, force fields, classification, computational methods, and structure prediction. Each chapter is a self contained review covering definition of the problem and historical perspective; mathematical formulation; computational methods and algorithms; performance results; existing software; strengths, pitfalls, challenges, and future research.
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 : David Webster
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-02-03
Protein Structure Prediction written by David Webster 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 2008-02-03 with Science categories.
The number of protein sequences grows each year, yet the number of structures deposited in the Protein Data Bank remains relatively small. The importance of protein structure prediction cannot be overemphasized, and this volume is a timely addition to the literature in this field. Protein Structure Prediction: Methods and Protocols is a departure from the normal Methods in Molecular Biology series format. By its very nature, protein structure prediction demands that there be a greater mix of theoretical and practical aspects than is normally seen in this series. This book is aimed at both the novice and the experienced researcher who wish for detailed inf- mation in the field of protein structure prediction; a major intention here is to include important information that is needed in the day-to-day work of a research scientist, important information that is not always decipherable in scientific literature. Protein Structure Prediction: Methods and Protocols covers the topic of protein structure prediction in an eclectic fashion, detailing aspects of pred- tion that range from sequence analysis (a starting point for many algorithms) to secondary and tertiary methods, on into the prediction of docked complexes (an essential point in order to fully understand biological function). As this volume progresses, the authors contribute their expert knowledge of protein structure prediction to many disciplines, such as the identification of motifs and domains, the comparative modeling of proteins, and ab initio approaches to protein loop, side chain, and protein prediction.
Computational Structural Biology Methods And Applications
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Author : Torsten Schwede
language : en
Publisher: World Scientific
Release Date : 2008-05-02
Computational Structural Biology Methods And Applications written by Torsten Schwede and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-05-02 with Science categories.
Computational structural biology has made tremendous progress over the last two decades, and this book provides a recent and broad overview of such computational methods in structural biology. It covers the impact of computational structural biology on protein structure prediction methods, macromolecular function and protein design, and key methods in drug discovery. It also addresses the computational challenges of experimental approaches in structural biology. In addition to reviewing the current state of computational structural biology, each chapter ends with a brief, visionary discussion on the future outlook, whereby the main challenges for the coming years are elucidated. Written by an international panel of expert contributors, this book can serve as a reference manual for students and practitioners alike.
Alphafold 3 A Revolution In Protein Structure Prediction
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Author : StoryBuddiesPlay
language : en
Publisher: StoryBuddiesPlay
Release Date : 2024-05-19
Alphafold 3 A Revolution In Protein Structure Prediction written by StoryBuddiesPlay and has been published by StoryBuddiesPlay this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-05-19 with Computers categories.
AlphaFold 3: Unveiling the Secrets of Life, One Molecule at a Time Demystifying the intricate world of proteins just got a whole lot easier with the arrival of AlphaFold 3. This groundbreaking AI model, developed by DeepMind and Isomorphic Labs, has revolutionized protein structure prediction, a field that has captivated scientists for decades. No longer limited to laborious experimental methods, AlphaFold 3 utilizes the power of deep learning to accurately predict protein structures from their amino acid sequences. This capability unlocks a treasure trove of possibilities for various scientific disciplines. From accelerating drug discovery and personalized medicine to understanding complex diseases and designing novel biomaterials, AlphaFold 3 stands poised to transform our understanding of life at the molecular level. Here's what you'll discover in this comprehensive guide: The Protein Folding Problem Explained: Dive into the challenges of traditionally predicting protein structures and the significance of solving this scientific puzzle. The Rise of Deep Learning: A New Hope for Protein Science: Explore how deep learning has emerged as a powerful tool for tackling complex scientific problems like protein structure prediction. A Deep Dive into AlphaFold: Birth of a Revolutionary AI Model: Learn about the development of AlphaFold by DeepMind, its groundbreaking architecture, and its impact on the scientific community. From AlphaFold 2 to AlphaFold 3: Pushing the Boundaries of Accuracy: Witness the continuous advancements in AlphaFold's capabilities, culminating in AlphaFold 3's ability to predict structures of a wider range of biomolecules beyond proteins. Revolutionizing Drug Discovery: How AlphaFold 3 is Changing the Game: Discover how AlphaFold 3 is accelerating the identification and design of new drugs by providing precise structural insights into protein-drug interactions. Unlocking the Secrets of Diseases: A New Lens for Diagnosis and Treatment: Explore how AlphaFold 3 is transforming our understanding of diseases at the molecular level, paving the way for earlier diagnosis, personalized medicine, and the development of new therapies. Beyond Proteins: Expanding the Horizons of AlphaFold 3: Uncover the exciting potential of AlphaFold 3 in predicting the structures of DNA, RNA, and other biomolecules, leading to a more holistic view of cellular processes. The Future of Protein Science: A Collaborative and Responsible Approach: Delve into the ethical considerations surrounding AlphaFold 3 and the importance of responsible development, open access, and international collaboration to maximize its benefits for humanity. This blog post goes beyond just summarizing the features of AlphaFold 3. It provides a compelling narrative that explores the history, scientific significance, and future potential of this groundbreaking technology. Whether you're a scientist, student, or simply curious about the future of scientific discovery, this guide offers a comprehensive exploration of AlphaFold 3 and its transformative impact on the world of science.