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Comparison Of Protein Secondary Structure Prediction Algorithms
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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 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.
Book Synopsis Computer Assisted Modeling by : National Research Council
Download or read book Computer Assisted Modeling written by National Research Council and published by National Academies Press. This book was released on 1987-02-01 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: In much of biology, the search for understanding the relation between structure and function is now taking place at the macromolecular level. Proteins, nucleic acids, and polysaccharides are macromolecule--polymers formed from families of simpler subunits. Because of their size and complexity, the polymers are capable of both inter- and intramolecular interactions. These interactions confer upon the polymers distinctive three-dimensional shapes. These tertiary configurations, in turn, determine the function of the macromolecule. Computers have become so inextricably involved in empirical studies of three-dimensional macromolecular structure that mathematical modeling, or theory, and experimental approaches are interrelated aspects of a single enterprise.
Book Synopsis Mathematical Methods for Protein Structure Analysis and Design by : Concettina Guerra
Download or read book Mathematical Methods for Protein Structure Analysis and Design written by Concettina Guerra and published by Springer Science & Business Media. This book was released on 2003-06-25 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: The papers collected in this volume reproduce contributions by leading sch- arstoaninternationalschoolandworkshopwhichwasorganizedandheldwith thegoaloftakinga snapshotofadiscipline undertumultuous growth. Indeed, the area of protein folding, docking and alignment is developing in response to needs for a mix of heterogeneous expertise spanning biology, chemistry, mathematics, computer science, and statistics, among others. Some of the problems encountered in this area are not only important for the scienti?c challenges they pose, but also for the opportunities they disclose intermsofmedicalandindustrialexploitation. Atypicalexampleiso?eredby protein-drug interaction (docking), a problem posing daunting computational problems at the crossroads of geometry, physics and chemistry, and, at the same time, a problem with unimaginable implications for the pharmacopoeia of the future. The schoolfocused on problems posed by the study of the mechanisms - hind protein folding, and explored di?erent ways of attacking these problems under objective evaluations of the methods. Together with a relatively small core of consolidated knowledge and tools, important re?ections were brought to this e?ort by studies in a multitude of directions and approaches. It is obviously impossible to predict which, if any, among these techniques will prove completely successful, but it is precisely the implicit dialectic among them that best conveys the current ?avor of the ?eld. Such unique diversity and richness inspired the format of the meeting, and also explains the slight departure of the present volume from the typical format in this series: the exposition of the current sediment is complemented here by a selection of quali?ed specialized contributions.
Book Synopsis Biological Sequence Analysis by : Richard Durbin
Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.
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 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 Practical Bioinformatics by : Janusz M. Bujnicki
Download or read book Practical Bioinformatics written by Janusz M. Bujnicki and published by Springer Science & Business Media. This book was released on 2004-03-03 with total page 292 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bridges the gap between bioinformaticists and molecular biologists, i.e. the developers and the users of computational methods for biological data analysis and in that it presents examples of practical applications of the bioinformatics tools in the "daily practice" of an experimental research scientist.
Book Synopsis Protein Structure Prediction by : Mohammed Zaki
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.
Book Synopsis Algorithms and Architectures for Parallel Processing by : Arrems Hua
Download or read book Algorithms and Architectures for Parallel Processing written by Arrems Hua and published by Springer Science & Business Media. This book was released on 2009-07-10 with total page 896 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 9th International Conference on Algorithms and Architectures for Parallel Processing, ICA3PP 2009, held in Taipei, Taiwan, in June 2009. The 80 revised full papers were carefully reviewed and selected from 243 submissions. The papers are organized in topical sections on bioinformatics in parallel computing; cluster, grid and fault-tolerant computing; cluster distributed parallel operating systems; dependability issues in computer networks and communications; dependability issues in distributed and parallel systems; distributed scheduling and load balancing, industrial applications; information security internet; multi-core programming software tools; multimedia in parallel computing; parallel distributed databases; parallel algorithms; parallel architectures; parallel IO systems and storage systems; performance of parallel ditributed computing systems; scientific applications; self-healing, self-protecting and fault-tolerant systems; tools and environments for parallel and distributed software development; and Web service.
Book Synopsis Protein Bioinformatics by : M. Michael Gromiha
Download or read book Protein Bioinformatics written by M. Michael Gromiha and published by Academic Press. This book was released on 2011-04-21 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the most pressing tasks in biotechnology today is to unlock the function of each of the thousands of new genes identified every day. Scientists do this by analyzing and interpreting proteins, which are considered the task force of a gene. This single source reference covers all aspects of proteins, explaining fundamentals, synthesizing the latest literature, and demonstrating the most important bioinformatics tools available today for protein analysis, interpretation and prediction. Students and researchers of biotechnology, bioinformatics, proteomics, protein engineering, biophysics, computational biology, molecular modeling, and drug design will find this a ready reference for staying current and productive in this fast evolving interdisciplinary field. - Explains all aspects of proteins including sequence and structure analysis, prediction of protein structures, protein folding, protein stability, and protein interactions - Presents a cohesive and accessible overview of the field, using illustrations to explain key concepts and detailed exercises for students.
Book Synopsis Circular Dichroism and the Conformational Analysis of Biomolecules by : G.D. Fasman
Download or read book Circular Dichroism and the Conformational Analysis of Biomolecules written by G.D. Fasman and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 739 pages. Available in PDF, EPUB and Kindle. Book excerpt: ''Excellent and very timely....It will undoubtedly become a standard reference for the application of circular dichroism (CD) to biomolecules.'' --- Quarterly Review of Biology, March 1997 ''[T]estament to the book's utility is the fact that during the course of my review I had to 'rescue' it from the desks of graduate students on an almost daily basis. In summary, this is a great book.'' --- American Scientist ''Well documented chapters provide a very good insight into the problems surrounding the conformation of biomacromolecules...An indispensible source of information.'' --- Nahrung, 42(2), 1998 Renowned experts present the first state-of-the-art description of circular dichroism spectroscopy (CD). Chapters present in-depth discussions of the history of the field, the theory of CD for application to globular proteins, membrane proteins, peptides, nucleic acids and their interactions, carbohydrates, and instrumentation. Discussions also feature new techniques using synchrotron radiation, vibrational Raman optical activity, and vibrational CD. More than 250 illustrations supplement the text.
Book Synopsis RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods by : Jan Gorodkin
Download or read book RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods written by Jan Gorodkin and published by Humana. This book was released on 2014-03-18 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes. However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere. However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results. Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics.
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.
Download or read book Computational Methods written by G.R. Liu and published by Springer Science & Business Media. This book was released on 2007-05-26 with total page 954 pages. Available in PDF, EPUB and Kindle. Book excerpt: The First International Conference on Computational Methods (ICCM04), organized by the department of Mechanical Engineering, National University of Singapore, was held in Singapore, December 15-17, 2004, with great success. This conference proceedings contains some 290 papers from more than 30 countries/regions. The papers cover a broad range of topics such as meshfree particle methods, Generalized FE and Extended FE methods, inverse analysis and optimization methods. Computational methods for geomechanics, machine learning, vibration, shock, impact, health monitoring, material modeling, fracture and damage mechanics, multi-physics and multi-scales simulation, sports and environments are also included. All the papers are pre-reviewed before they are accepted for publication in this proceedings. The proceedings will provide an informative, timely and invaluable resource for engineers and scientists working in the important areas of computational methods.
Book Synopsis Advances in Protein Molecular and Structural Biology Methods by : Timir Tripathi
Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. - Presents a thorough overview of the latest and emerging methods and technologies for protein study - Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy - Includes computational and machine learning methods - Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins
Book Synopsis Multistrategy Learning by : Ryszard S. Michalski
Download or read book Multistrategy Learning written by Ryszard S. Michalski and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: Most machine learning research has been concerned with the development of systems that implememnt one type of inference within a single representational paradigm. Such systems, which can be called monostrategy learning systems, include those for empirical induction of decision trees or rules, explanation-based generalization, neural net learning from examples, genetic algorithm-based learning, and others. Monostrategy learning systems can be very effective and useful if learning problems to which they are applied are sufficiently narrowly defined. Many real-world applications, however, pose learning problems that go beyond the capability of monostrategy learning methods. In view of this, recent years have witnessed a growing interest in developing multistrategy systems, which integrate two or more inference types and/or paradigms within one learning system. Such multistrategy systems take advantage of the complementarity of different inference types or representational mechanisms. Therefore, they have a potential to be more versatile and more powerful than monostrategy systems. On the other hand, due to their greater complexity, their development is significantly more difficult and represents a new great challenge to the machine learning community. Multistrategy Learning contains contributions characteristic of the current research in this area.
Book Synopsis RNA 3D Structure Analysis and Prediction by : Neocles Leontis
Download or read book RNA 3D Structure Analysis and Prediction written by Neocles Leontis and published by Springer Science & Business Media. This book was released on 2012-06-05 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.
