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.

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.

Download or read book Protein Structure Prediction written by Mohammed Zaki and published by Springer Science & Business Media. This book was released on 2007-09-12 with total page 338 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers elements of both the data-driven comparative modeling approach to structure prediction and also recent attempts to simulate folding using explicit or simplified models. Despite the unsolved mystery of how a protein folds, advances are being made in predicting the interactions of proteins with other molecules. Also rapidly advancing are the methods for solving the inverse folding problem, the problem of finding a sequence to fit a structure. This book focuses on the various computational methods for prediction, their successes and their limitations, from the perspective of their most well known practitioners.

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.

Download or read book Molecular Modeling and Simulation written by Tamar Schlick and published by Springer Science & Business Media. This book was released on 2013-04-18 with total page 669 pages. Available in PDF, EPUB and Kindle. Book excerpt: Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text

Download or read book Special Issue on Ionic Channels II written by M. P. Blaustein and published by Springer. This book was released on 2013-12-01 with total page 143 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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:

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.

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. -

Download or read book First Principles Prediction of Structures and Properties in Crystals written by Dominik Kurzydlowsk and published by MDPI. This book was released on 2019-10-25 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: The term “first-principles calculations” is a synonym for the numerical determination of the electronic structure of atoms, molecules, clusters, or materials from ‘first principles’, i.e., without any approximations to the underlying quantum-mechanical equations. Although numerous approximate approaches have been developed for small molecular systems since the late 1920s, it was not until the advent of the density functional theory (DFT) in the 1960s that accurate “first-principles” calculations could be conducted for crystalline materials. The rapid development of this method over the past two decades allowed it to evolve from an explanatory to a truly predictive tool. Yet, challenges remain: complex chemical compositions, variable external conditions (such as pressure), defects, or properties that rely on collective excitations—all represent computational and/or methodological bottlenecks. This Special Issue comprises a collection of papers that use DFT to tackle some of these challenges and thus highlight what can (and cannot yet) be achieved using first-principles calculations of crystals.

Download or read book Reasoning Web written by Pedro Barahona and published by Springer Science & Business Media. This book was released on 2006-08-24 with total page 279 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents thoroughly arranged tutorial papers corresponding to lectures given by leading researchers at the Second International Summer School on Reasoning Web in Lisbon, Portugal, in September 2006. Building on the predessor school held in 2005 and published as LNCS 3564, the ten tutorial lectures presented provide competent coverage of current topics in semantic Web research and development.

Download or read book Feature Representation and Learning Methods With Applications in Protein Secondary Structure written by Zhibin Lv and published by Frontiers Media SA. This book was released on 2021-10-25 with total page 112 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Special Issue on Emerging Bacterial Toxins written by Klaus Aktories and published by Springer Science & Business Media. This book was released on 2004-12-06 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: With contributions by numerous experts

Download or read book Biocomputing And Emergent Computation Proceedings Of Bcec97 written by Bjorn Olsson and published by World Scientific. This book was released on 1997-08-26 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains papers presented at the BCEC97 conference, held in Skövde, Sweden, in September 1997. The conference brought together researchers from biology and computer science to discuss the use of computational techniques in biology, as well as the use of biological metaphors in computing. Examples of the work presented in these papers include computer simulations of embryogenesis; algorithms for protein folding prediction; problem solving using DNA computation; neural-network learning in retina implants; and optimisation algorithms inspired by natural evolution.

Download or read book Prediction of Protein Structures Functions and Interactions written by Janusz M. Bujnicki and published by John Wiley & Sons. This book was released on 2008-12-23 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: The growing flood of new experimental data generated by genome sequencing has provided an impetus for the development of automated methods for predicting the functions of proteins that have been deduced by sequence analysis and lack experimental characterization. Prediction of Protein Structures, Functions and Interactions presents a comprehensive overview of methods for prediction of protein structure or function, with the emphasis on their availability and possibilities for their combined use. Methods of modeling of individual proteins, prediction of their interactions, and docking of complexes are put in the context of predicting gene ontology (biological process, molecular function, and cellular component) and discussed in the light of their contribution to the emerging field of systems biology. Topics covered include: first steps of protein sequence analysis and structure prediction automated prediction of protein function from sequence template-based prediction of three-dimensional protein structures: fold-recognition and comparative modelling template-free prediction of three-dimensional protein structures quality assessment of protein models prediction of molecular interactions: from small ligands to large protein complexes macromolecular docking integrating prediction of structure, function, and interactions Prediction of Protein Structures, Functions and Interactions focuses on the methods that have performed well in CASPs, and which are constantly developed and maintained, and are freely available to academic researchers either as web servers or programs for local installation. It is an essential guide to the newest, best methods for prediction of protein structure and functions, for researchers and advanced students working in structural bioinformatics, protein chemistry, structural biology and drug discovery.

Download or read book Biological Knowledge Discovery Handbook written by Mourad Elloumi and published by John Wiley & Sons. This book was released on 2013-12-24 with total page 1192 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first comprehensive overview of preprocessing, mining,and postprocessing of biological data Molecular biology is undergoing exponential growth in both thevolume and complexity of biological data—and knowledgediscovery offers the capacity to automate complex search and dataanalysis tasks. This book presents a vast overview of the mostrecent developments on techniques and approaches in the field ofbiological knowledge discovery and data mining (KDD)—providingin-depth fundamental and technical field information on the mostimportant topics encountered. Written by top experts, Biological Knowledge DiscoveryHandbook: Preprocessing, Mining, and Postprocessing of BiologicalData covers the three main phases of knowledge discovery (datapreprocessing, data processing—also known as datamining—and data postprocessing) and analyzes both verificationsystems and discovery systems. BIOLOGICAL DATA PREPROCESSING Part A: Biological Data Management Part B: Biological Data Modeling Part C: Biological Feature Extraction Part D Biological Feature Selection BIOLOGICAL DATA MINING Part E: Regression Analysis of Biological Data Part F Biological Data Clustering Part G: Biological Data Classification Part H: Association Rules Learning from Biological Data Part I: Text Mining and Application to Biological Data Part J: High-Performance Computing for Biological DataMining Combining sound theory with practical applications in molecularbiology, Biological Knowledge Discovery Handbook is idealfor courses in bioinformatics and biological KDD as well as forpractitioners and professional researchers in computer science,life science, and mathematics.

Download or read book The Crystalline States of Organic Compounds written by Angelo Gavezzotti and published by Elsevier. This book was released on 2021-11-25 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Crystalline States of Organic Compounds is a broad survey of the techniques by which molecular crystals are investigated, modeled, and applied, starting with the fundamentals of intra- and intermolecular bonding supplemented by a concise tutorial on present-day diffraction methods, then proceeding to an examination of crystallographic databases with their statistics and of such fundamental and fast-growing topics as intermolecular potentials, polymorphism, co-crystallization, and crystal structure prediction by computer. A substantial part of the book is devoted to the techniques of choice in modern simulation, Monte Carlo and molecular dynamics, with their most recent developments and application to formed crystals and to the concomitant phases involved in nucleation and growth. Drawing on the decades-long experience of its author in teaching and research in the field of organic solid state, The Crystalline States of Organic Compounds is an indispensable source of key insights and future directions for students and researchers at any level, in academia and in industry. - Condenses theoretical information and practical methods in a single resource - Provides a guide on the use of crystallographic databases, structure statistics, and molecular simulations - Includes a large number of worked examples and tutorials, with extensive graphics and multimedia