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A Multiobjective Approach Applied To The Protein Structure Prediction Problem
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Book Synopsis A Multiobjective Approach Applied to the Protein Structure Prediction Problem by : Richard O. Day
Download or read book A Multiobjective Approach Applied to the Protein Structure Prediction Problem written by Richard O. Day and published by . This book was released on 2002-03-01 with total page 228 pages. Available in PDF, EPUB and Kindle. Book excerpt: Interest in discovering a methodology for solving the Protein Structure Prediction problem extends into many fields of study including biochemistry, medicine, biology, and numerous engineering and science disciplines. Experimental approaches, such as, x-ray crystallographic studies or solution Nuclear Magnetic Resonance Spectroscopy, to mathematical modeling, such as minimum energy models are used to solve this problem. Recently, Evolutionary Algorithm studies at the Air Force Institute of Technology include the following: Simple Genetic Algorithm (GA), messy GA , fast messy GA, and Linkage Learning GA, as approaches for potential protein energy minimization. Prepackaged software like GENOCOP, GENESIS, and mGA are in use to facilitate experimentation of these techniques. In addition to this software, a parallelized version of the fmGA, the so-called parallel fast messy GA, is found to be good at finding semi-optimal answers in reasonable wall clock time. The aim of this work is to apply a Multiobjective approach to solving this problem using a modified fast messy GA. By dividing the CHARMm energy model into separate objectives, it should be possible to find structural configurations of a protein that yield lower energy values and ultimately more correct conformations.
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 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 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 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 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 Multiobjective Problem Solving from Nature by : Joshua Knowles
Download or read book Multiobjective Problem Solving from Nature written by Joshua Knowles and published by Springer Science & Business Media. This book was released on 2008-01-28 with total page 413 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text examines how multiobjective evolutionary algorithms and related techniques can be used to solve problems, particularly in the disciplines of science and engineering. Contributions by leading researchers show how the concept of multiobjective optimization can be used to reformulate and resolve problems in areas such as constrained optimization, co-evolution, classification, inverse modeling, and design.
Book Synopsis Protein Structure Prediction Based on Evolutionary Methods by : Alfonso E. Márquez Chamorro
Download or read book Protein Structure Prediction Based on Evolutionary Methods written by Alfonso E. Márquez Chamorro and published by LAP Lambert Academic Publishing. This book was released on 2013 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt: The problem of Protein Structure Prediction (PSP) is one of the principal topics in Bioinformatics. Multiple approaches have been developed in order to predict the protein structure of a protein. Determining the three dimensional structure of proteins is necessary to understand the functions of molecular protein level. An useful, and commonly used, representation for protein 3D structure is the protein contact map, which represents binary proximities (contact or non-contact) between each pair of amino acids of a protein. This book includes a compilation of the soft computing techniques for the protein structure prediction problem (secondary and tertiary structures). Two novel evolutionary structure predictors are also described in this work: a multi-objective evolutionary approach for contact map prediction and an evolutionary secondary structure predictor. Both of them are based on physico-chemical properties of amino acids. The evolutionary algorithms produce a set of decision rules that identifies contacts between amino acids and secondary structure motifs, respectively. Results obtained confirm the validity of our proposals.
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 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.
Book Synopsis Multiscale Approaches to Protein Modeling by : Andrzej Kolinski
Download or read book Multiscale Approaches to Protein Modeling written by Andrzej Kolinski and published by Springer Science & Business Media. This book was released on 2010-10-13 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book gives a comprehensive review of the most advanced multiscale methods for protein structure prediction, computational studies of protein dynamics, folding mechanisms and macromolecular interactions. It approaches span a wide range of the levels of coarse-grained representations, various sampling techniques and variety of applications to biomedical and biophysical problems. This book is intended to be used as a reference book for those who are just beginning their adventure with biomacromolecular modeling but also as a valuable source of detailed information for those who are already experts in the field of biomacromolecular modeling and in related areas of computational biology or biophysics.
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 Science & Business Media. This book was released on 2010-05-05 with total page 335 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 Parallel Computing for Bioinformatics and Computational Biology by : Albert Y. Zomaya
Download or read book Parallel Computing for Bioinformatics and Computational Biology written by Albert Y. Zomaya and published by John Wiley & Sons. This book was released on 2006-04-14 with total page 814 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discover how to streamline complex bioinformatics applications with parallel computing This publication enables readers to handle more complex bioinformatics applications and larger and richer data sets. As the editor clearly shows, using powerful parallel computing tools can lead to significant breakthroughs in deciphering genomes, understanding genetic disease, designing customized drug therapies, and understanding evolution. A broad range of bioinformatics applications is covered with demonstrations on how each one can be parallelized to improve performance and gain faster rates of computation. Current parallel computing techniques and technologies are examined, including distributed computing and grid computing. Readers are provided with a mixture of algorithms, experiments, and simulations that provide not only qualitative but also quantitative insights into the dynamic field of bioinformatics. Parallel Computing for Bioinformatics and Computational Biology is a contributed work that serves as a repository of case studies, collectively demonstrating how parallel computing streamlines difficult problems in bioinformatics and produces better results. Each of the chapters is authored by an established expert in the field and carefully edited to ensure a consistent approach and high standard throughout the publication. The work is organized into five parts: * Algorithms and models * Sequence analysis and microarrays * Phylogenetics * Protein folding * Platforms and enabling technologies Researchers, educators, and students in the field of bioinformatics will discover how high-performance computing can enable them to handle more complex data sets, gain deeper insights, and make new discoveries.
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 Multi-regional Analysis of Contact Maps for Protein Structure Prediction by : Hazem Radwan Abdal-Rehiem Ahmed
Download or read book Multi-regional Analysis of Contact Maps for Protein Structure Prediction written by Hazem Radwan Abdal-Rehiem Ahmed and published by . This book was released on 2009 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: 1D protein sequences, 2D contact maps and 3D structures are three different representational levels of detail for proteins. Predicting protein 3D structures from their 1D sequences remains one of the complex challenges of bioinformatics. The "Divide and Conquer" principle is applied in our research to handle this challenge, by dividing it into two separate yet dependent subproblems, using a Case-Based Reasoning (CBR) approach. Firstly, 2D contact maps are predicted from their 1D protein sequences; secondly, 3D protein structures are then predicted from their predicted 2D contact maps. We focus on the problem of identifying common substructural patterns of protein contact maps, which could potentially be used as building blocks for a bottom-up approach for protein structure prediction. We further demonstrate how to improve identifying these patterns by combining both protein sequence and structural information. We assess the consistency and the efficiency of identifying common substructural patterns by conducting statistical analyses on several subsets of the experimental results with different sequence and structural information.
Book Synopsis 2002 International Conference on Computational Nanoscience and Nanotechnology by : Matthew Laudon
Download or read book 2002 International Conference on Computational Nanoscience and Nanotechnology written by Matthew Laudon and published by . This book was released on 2002 with total page 550 pages. Available in PDF, EPUB and Kindle. Book excerpt: The worlds most comprehensive and up-to-date collection of Nanotechnology and Nanoscience technical papers. Technical Proceedings of the Nanotech 2002 and the International Conference on Computational Nanoscience and Nanotechnology. Nanotech Vol. 1: Sequence and Biological Structure, Computer Aided Drug Design, Biological Conduction Processes, Biotechnology, Micro and Nano Fluidic Systems, Soft Condensed Matter, Extedned-Scale Atomistics, Quantum Effects, Quantum Devices, Spintronics, Mechanical Properties at the Nanoscale, Molecular and Nano Electronics, Condensed Matter Phenomena, Process Modeling, Nanotechnology, Materials and Nanostructures Studies, Nano Particles and Molecules. Papers taken from the 2002 Nanotechnology Conference and Trade Show, San Juan, Puerto Rico, April. 2002.
Book Synopsis Optimizing Potentials for Protein Structure Prediction, Inverse Protein Folding and Protein Folding by : Ting-Lan Chiu
Download or read book Optimizing Potentials for Protein Structure Prediction, Inverse Protein Folding and Protein Folding written by Ting-Lan Chiu and published by . This book was released on 1999 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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.
