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Prediction De La Structure Des Proteines Par Homologie
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Book Synopsis Prédiction de la structure des protéines par homologie by : Jonathan Mark Levin
Download or read book Prédiction de la structure des protéines par homologie written by Jonathan Mark Levin and published by . This book was released on 1989 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ce travail présente de nouvelles méthodes pour extraire des informations structurales à partir d'une séquence en acides aminés et l'application de ces méthodes à la modélisation des protéines. Nous avons mis au point un algorithme d'alignement multiple pour des séquences protéiques basé sur l'algorithme de Needleman et Wunsch, mais qui n'est pas limité par le nombre et la taille des séquences protéiques à aligner. Nous avons développé une méthode de prédiction des structures secondaires, la Méthode des Homologues, basée sur les similarités entre peptides, qui prédit correctement 63% des résidus d'acides aminés, pour trois états. Cette méthode prédit correctement 87% des résidus d'une protéine homologue avec une protéine de la base de données. Nous avons utilisé un modèle simplifié de la chaîne polypeptique pour déterminer les limites des calculs par minimisation de l'énergie. Nous avons appliqué ces techniques à la modélisation des protéines de choc thermique (HSP90), du domaine liant l'ADN des protéines régulatrices FixK et Fnr et du domaine liant l'hème de la nitrate réductase de tabac.
Book Synopsis Prediction of Protein Structure and the Principles of Protein Conformation by : G.D. Fasman
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.
Book Synopsis Introduction to Protein Structure Prediction by : Huzefa Rangwala
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.
Book Synopsis Protein Structure Prediction by : Igor F. Tsigelny
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:
Book Synopsis Protein Structure Prediction : A Practical Approach by : Michael J. E. Sternberg
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. -
Book Synopsis Protein Structure Prediction by : David Webster
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.
Book Synopsis Prediction of Protein Secondary Structure by : Yaoqi Zhou
Download or read book Prediction of Protein Secondary Structure written by Yaoqi Zhou and published by Humana. This book was released on 2018-06-08 with total page 313 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.
Book Synopsis NOUVELLES STRATEGIES D'ANALYSE ET DE PREDICTION DES STRUCTURES TRIDIMENSIONNELLES DES PROTEINES by : ALEXANDRE.. DE BREVERN
Download or read book NOUVELLES STRATEGIES D'ANALYSE ET DE PREDICTION DES STRUCTURES TRIDIMENSIONNELLES DES PROTEINES written by ALEXANDRE.. DE BREVERN and published by . This book was released on 2001 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt: LA REPRESENTATION DE LA STRUCTURE TRIDIMENSIONNELLE DES PROTEINES CLASSIQUEMENT CARACTERISEE AVEC 3 ETATS DISTINCTS (HELICE, FEUILLET, BOUCLE) DEMEURE ASSEZ PAUVRE STRUCTURELLEMENT. NOUS AVONS DONC DEVELOPPE UNE NOUVELLE METHODOLOGIE POUR CONCEVOIR DES SERIES DE PETITS PROTOTYPES MOYENS NOMMES BLOCS PROTEIQUES (BPS) POUR PERMETTRE UNE APPROXIMATION CORRECTE DES STRUCTURES PROTEIQUES ASSOCIEE A UNE PREDICTION LOCALE ACCEPTABLE. L'ANALYSE DE LA SPECIFICITE DES BPS SUR LE PLAN DE LEUR STABILITE ET STRUCTURALE, DE LEUR COMPOSITION EN ACIDES AMINES ET LES COMPARAISONS AVEC D'AUTRES ALPHABETS EXISTANTS ONT ETE REALISEES PAR LA SUITE. CETTE PREDICTION LOCALE DE LA STRUCTURE PROTEIQUE EN TERMES DE BPS SE FONDE SUR UNE METHODE BAYESIENNE QUI PERMET DE COMPRENDRE LES AFFINITES DES ACIDES AMINES DE MANIERE SIMPLE. POUR AMELIORER CETTE PREDICTION, NOUS NOUS SOMMES BASES SUR DEUX CONCEPTS : (I) 1 REPLIEMENT LOCAL -> N SEQUENCES ET (II) 1 SEQUENCE -> N REPLIEMENTS. LE PREMIER CONCEPT SIGNIFIE QUE PLUSIEURS TYPES DE SEQUENCES PEUVENT ETRE ASSOCIES A LA MEME STRUCTURE ET LE SECOND QU'UNE SEQUENCE PEUT ETRE ASSOCIEE A PLUSIEURS TYPE DE REPLIEMENTS. CES DEUX ASPECTS SONT DEVELOPPES EN SE BASANT SUR LA RECHERCHE D'UN INDICE DE FIABILITE DE LA PREDICTION LOCALE, POUR TROUVER DES ZONES DE FORTE PREDICTIBILITE. CERTAINS MOTS, I.E. SUCCESSIONS DE BPS APPARAISSANT FREQUEMMENT NOUS ONT PERMIS DE DEFINIR UN GRAPHE DE LIAISON DES BPS DECRIVANT AU MIEUX L'ARCHITECTURE DES DOMAINES PROTEIQUES. DU FAIT DE CETTE REDONDANCE QUI PEUT APPARAITRE DANS LA STRUCTURE PROTEIQUE, UNE METHODE DE COMPACTAGE QUI PERMET D'ASSOCIER DES STRUCTURES STRUCTURELLEMENT PROCHES SUR LE PLAN LOCAL A ETE MISE AU POINT. CETTE APPROCHE APPELEE PROTEINE HYBRIDE DE CONCEPTION SIMPLE PERMET DE CATEGORISER EN CLASSES STRUCTURELLEMENT DEPENDANTES L'ENSEMBLE DES STRUCTURES DE LA BASE DE DONNEES PROTEIQUES. CETTE APPROCHE PEUT ETRE UTILISEE DANS LA RECHERCHE D'HOMOLOGIE STRUCTURALE ET DES DEPENDANCES ENTRE STRUCTURES ET SEQUENCES.
Book Synopsis Protein Structure Prediction Using a Combination of Sequence Homology and Global Energy Minimization by : Michael J. Dudek
Download or read book Protein Structure Prediction Using a Combination of Sequence Homology and Global Energy Minimization written by Michael J. Dudek and published by . This book was released on 1989 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis A Metaheuristic Approach to Protein Structure Prediction by : Nanda Dulal Jana
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.
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.
Book Synopsis Protein Structure Prediction by : Anna Tramontano
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.
Book Synopsis PREDICTION DE LA STRUCTURE SECONDAIRE DES PROTEINES PAR ANALYSE SPECTRALE DE LA SEQUENCE D'HYDROPHOBICITE by : PATRICK.. ROMANET
Download or read book PREDICTION DE LA STRUCTURE SECONDAIRE DES PROTEINES PAR ANALYSE SPECTRALE DE LA SEQUENCE D'HYDROPHOBICITE written by PATRICK.. ROMANET and published by . This book was released on 1999 with total page 168 pages. Available in PDF, EPUB and Kindle. Book excerpt: CE TRAVAIL PRESENTE TROIS METHODES DE PREDICTION DE LA STRUCTURE SECONDAIRE DES PROTEINES PAR ANALYSE SPECTRALE DE LA SEQUENCE D'HYDROPHOBICITE. UNE ETUDE COMPARATIVE PRELIMINAIRE SUR 41 ECHELLES D'HYDROPHOBICITE AINSI QUE SUR DIFFERENTES METHODES D'ANALYSE SPECTRALE CLASSIQUES ET PARAMETRIQUES A ETE MENEE POUR DETERMINER L'ECHELLE OPTIMALE ET LA METHODE SPECTRALE LA MIEUX ADAPTEE A CHAQUE TYPE DE PREDICTION. LES PARAMETRES DES METHODES DE PREDICTION ONT ETE EVALUES A PARTIR D'UNE BASE DE DONNEES, COMPORTANT 1028 CHAINES PEPTIDIQUES AYANT MOINS DE 25% D'HOMOLOGIE (223157 RESIDUS). LES TROIS METHODES MISES AU POINT CONSISTENT EN : 1) UNE PREDICTION GLOBALE SUR UNE PROTEINE OU UN SEGMENT PROTEIQUE, DONNANT 53.5% DE BONNES PREDICTIONS SELON QUATRE CONFORMATIONS : HELICES ALPHA (H), FEUILLETS BETA (B), STRUCTURES ALEATOIRES (C) ET HELICES PLUS FEUILLETS (HB), 2) UNE PREDICTION LOCALISEE DES HELICES ET DES FEUILLETS SANS TENIR COMPTE DES RESIDUS DE STRUCTURE ALEATOIRE (80% DE BONNES PREDICTIONS SELON TROIS CONFORMATIONS : H, B ET HB) ET 3) UNE PREDICTION ACIDE AMINE PAR ACIDE AMINE (41.75% DE BONNES PREDICTIONS SUR TROIS CONFORMATIONS : H, B ET C). POUR CETTE DERNIERE METHODE, ON PEUT CALCULER LA FIABILITE DE PREDICTION DE CHAQUE RESIDU. L'INTRODUCTION D'UN SEUIL AUGMENTE LA FIABILITE DE PREDICTION SUR UN NOMBRE REDUIT DE RESIDUS (PAR EXEMPLE EN FIXANT LE SEUIL DE PREDICTION DES HELICES A 70% ON OBTIENT 65.5% DE BONNES PREDICTIONS SUR 8.31% DES RESIDUS).
Book Synopsis Protein Structure Prediction by : Hyun Soon Gweon
Download or read book Protein Structure Prediction written by Hyun Soon Gweon and published by . This book was released on 2008 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Computational Methods for Protein Structure Prediction and Modeling by : Ying Xu
Download or read book Computational Methods for Protein Structure Prediction and Modeling written by Ying Xu and published by Springer. This book was released on 2010-12-01 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume Two of this two-volume sequence presents a comprehensive overview of protein structure prediction methods and includes protein threading, De novo methods, applications to membrane proteins and protein complexes, structure-based drug design, as well as structure prediction as a systems problem. A series of appendices review the biological and chemical basics related to protein structure, computer science for structural informatics, and prerequisite mathematics and statistics.
Book Synopsis Homology-based Protein Structure Prediction by : Yuling An
Download or read book Homology-based Protein Structure Prediction written by Yuling An and published by . This book was released on 2002 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Utilization of Protein Tertiary Contacts to Improve Protein Structure Prediction Using Sequence Homology by : Trung Thanh Nguyen
Download or read book Utilization of Protein Tertiary Contacts to Improve Protein Structure Prediction Using Sequence Homology written by Trung Thanh Nguyen and published by . This book was released on 2012 with total page 159 pages. Available in PDF, EPUB and Kindle. Book excerpt: The structure of a protein ultimately determines its function; therefore, knowledge of three-dimensional structure is essential for understanding its function and mechanism of action. The two most common methods for determining protein structure are x-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy. These methods are quite successful but can be very time-intensive and costly. An alternative method is protein structure prediction, where structure is computationally predicted from amino acid sequence. As opposed to x-ray crystallography and NMR spectroscopy, protein structure prediction is not encumbered by potential experimental problems. In this research, we attempted to determine if certain protein structure features, known as tertiary contacts, can improve the prediction of protein three-dimensional structure. By calculating and analyzing sequence homology and related values, it was shown that tertiary contacts, which typically are long-range amino acid interactions separated by at least 10 amino acids in sequence length, generally have lower pair averaged sequence homology-based values. From our calculations we were able to create a prediction filter based on our known literature-derived tertiary contacts of whether amino acid residues are buried or on the surface of a protein. From our tertiary contact prediction filter, it was shown that approximately 80% of the amino acid residues in our protein learning set were correctly filtered to be on the surface of a protein. These results imply that tertiary contacts are more conserved, densely packed, and less likely to be on the surface of a protein. From the tertiary contact prediction filter, we hope that tertiary contacts can be utilized in conjunction with other prediction approaches to more accurately predict where amino acids may be located in a protein.
