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Author : Yoonjoo Choi
Publisher :
ISBN 13 :
Total Pages : 314 pages
Book Rating : 4.:/5 (951 download)
Download or read book Protein Loop Structure Prediction written by Yoonjoo Choi and published by . This book was released on 2011 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Huzefa Rangwala
Publisher : John Wiley & Sons
ISBN 13 : 111809946X
Total Pages : 611 pages
Book Rating : 4.1/5 (18 download)
Download or read book Introduction to Protein Structure Prediction written by Huzefa Rangwala and published by John Wiley & Sons. This book was released on 2011-03-16 with total page 611 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : David Webster
Publisher : Springer Science & Business Media
ISBN 13 : 1592593682
Total Pages : 425 pages
Book Rating : 4.5/5 (925 download)
Download or read book Protein Structure Prediction written by David Webster and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Igor F. Tsigelny
Publisher : Internat'l University Line
ISBN 13 : 9780963681775
Total Pages : 540 pages
Book Rating : 4.6/5 (817 download)
Download or read book Protein Structure Prediction written by Igor F. Tsigelny and published by Internat'l University Line. This book was released on 2002 with total page 540 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Martin Monnigmann
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (129 download)
Download or read book Protein Loop Structure Prediction with Flexible Stem Geometries written by Martin Monnigmann and published by . This book was released on 2005 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : G.D. Fasman
Publisher : Springer Science & Business Media
ISBN 13 : 1461315719
Total Pages : 796 pages
Book Rating : 4.4/5 (613 download)
Download or read book Prediction of Protein Structure and the Principles of Protein Conformation written by G.D. Fasman and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 796 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : David Wales
Publisher : Cambridge University Press
ISBN 13 : 9780521814157
Total Pages : 696 pages
Book Rating : 4.8/5 (141 download)
Download or read book Energy Landscapes written by David Wales and published by Cambridge University Press. This book was released on 2003 with total page 696 pages. Available in PDF, EPUB and Kindle. Book excerpt: A self-contained account of energy landscape theory aimed at graduate students and researchers.
Author : Michael J. E. Sternberg
Publisher : Oxford University Press, USA
ISBN 13 : 0191588997
Total Pages : 322 pages
Book Rating : 4.1/5 (915 download)
Download or read book Protein Structure Prediction : A Practical Approach written by Michael J. E. Sternberg and published by Oxford University Press, USA. This book was released on 1996-11-28 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 prediction of the three-dimensional structure of a protein from its sequence is a problem faced by an ever-increasing number of biological scientists as they strive to utilize genetic information. The increasing sizes of the sequence and structural databases, the improvements in computing power, and the deeper understanding of the principles of protein structure have led to major developments in the field in the last few years. This book presents practical computer-based methods using the latest computer modelling algorithms. -
Author : Ying Xu
Publisher : Springer Science & Business Media
ISBN 13 : 0387683720
Total Pages : 408 pages
Book Rating : 4.3/5 (876 download)
Download or read book Computational Methods for Protein Structure Prediction and Modeling written by Ying Xu and published by Springer Science & Business Media. This book was released on 2007-08-24 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Douglas Gene Wardell
Publisher :
ISBN 13 :
Total Pages : 106 pages
Book Rating : 4.:/5 (657 download)
Download or read book A Distance-based Scoring Function for Protein Loop Structure Prediction written by Douglas Gene Wardell and published by . This book was released on 2009 with total page 106 pages. Available in PDF, EPUB and Kindle. Book excerpt: Describes a process whereby a new scoring function may be generated for the prediction of protein loop stuctures. Derives the function by analyzing the distance distributions between specific atoms within the loops of a large collection of known proteins and combining them using the kernel distance estimation (KDE) formula to estimate a protein density estimate which can be used by the inverse Boltzmann law to generate a potential energy function.
Author : Yaoqi Zhou
Publisher : Humana
ISBN 13 : 9781493964048
Total Pages : 0 pages
Book Rating : 4.9/5 (64 download)
Download or read book Prediction of Protein Secondary Structure written by Yaoqi Zhou and published by Humana. This book was released on 2016-10-28 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thorough volume explores predicting one-dimensional functional properties, functional sites in particular, from protein sequences, an area which is getting more and more attention. Beginning with secondary structure prediction based on sequence only, the book continues by exploring secondary structure prediction based on evolution information, prediction of solvent accessible surface areas and backbone torsion angles, model building, global structural properties, functional properties, as well as visualizing interior and protruding regions in proteins. Written for the highly successful Methods in Molecular Biology series, the chapters include the kind of detail and implementation advice to ensure success in the laboratory. Practical and authoritative, Prediction of Protein Secondary Structure serves as a vital guide to numerous state-of-the-art techniques that are useful for computational and experimental biologists.
Author : Kenneth M.Jr. Merz
Publisher : Springer Science & Business Media
ISBN 13 : 1468468316
Total Pages : 585 pages
Book Rating : 4.4/5 (684 download)
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.
Author : Pascal Benkert
Publisher :
ISBN 13 :
Total Pages : 209 pages
Book Rating : 4.:/5 (222 download)
Download or read book Protein Structure Prediction written by Pascal Benkert and published by . This book was released on 2007 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Daniel John Rigden
Publisher : Springer Science & Business Media
ISBN 13 : 1402090587
Total Pages : 330 pages
Book Rating : 4.4/5 (2 download)
Download or read book From Protein Structure to Function with Bioinformatics written by Daniel John Rigden and published by Springer Science & Business Media. This book was released on 2008-12-11 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Anna Tramontano
Publisher : John Wiley & Sons
ISBN 13 : 352731167X
Total Pages : 226 pages
Book Rating : 4.5/5 (273 download)
Download or read book Protein Structure Prediction written by Anna Tramontano and published by John Wiley & Sons. This book was released on 2006-02-20 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: While most textbooks on bioinformatics focus on genetic algorithms and treat protein structure prediction only superficially, this course book assumes a novel and unique focus. Adopting a didactic approach, the author explains all the current methods in terms of their reliability, limitations and user-friendliness. She provides practical examples to help first-time users become familiar with the possibilities and pitfalls of computer-based structure prediction, making this a must-have for students and researchers.
Author : Nanda Dulal Jana
Publisher : Springer
ISBN 13 : 3319747754
Total Pages : 243 pages
Book Rating : 4.3/5 (197 download)
Download or read book A Metaheuristic Approach to Protein Structure Prediction written by Nanda Dulal Jana and published by Springer. This book was released on 2018-03-05 with total page 243 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book introduces characteristic features of the protein structure prediction (PSP) problem. It focuses on systematic selection and improvement of the most appropriate metaheuristic algorithm to solve the problem based on a fitness landscape analysis, rather than on the nature of the problem, which was the focus of methodologies in the past. Protein structure prediction is concerned with the question of how to determine the three-dimensional structure of a protein from its primary sequence. Recently a number of successful metaheuristic algorithms have been developed to determine the native structure, which plays an important role in medicine, drug design, and disease prediction. This interdisciplinary book consolidates the concepts most relevant to protein structure prediction (PSP) through global non-convex optimization. It is intended for graduate students from fields such as computer science, engineering, bioinformatics and as a reference for researchers and practitioners.
Author : Vinu V Das
Publisher : Springer
ISBN 13 : 3642195423
Total Pages : 689 pages
Book Rating : 4.6/5 (421 download)
Download or read book Computer Networks and Information Technologies written by Vinu V Das and published by Springer. This book was released on 2011-03-15 with total page 689 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the Second International Conference on Advances in Communication, Network, and Computing, CNC 2011, held in Bangalore, India, in March 2011. The 41 revised full papers, presented together with 50 short papers and 39 poster papers, were carefully reviewed and selected for inclusion in the book. The papers feature current research in the field of Information Technology, Networks, Computational Engineering, Computer and Telecommunication Technology, ranging from theoretical and methodological issues to advanced applications.
