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Implementation Of Genetic Algorithms For Protein Structure Prediction Based On Lattice Models
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Book Synopsis Implementation of Genetic Algorithms for Protein Structure Prediction Based on Lattice Models by : 李俍叡
Download or read book Implementation of Genetic Algorithms for Protein Structure Prediction Based on Lattice Models written by 李俍叡 and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Memetic Approach for Prediction of Low Resolution Protein Structures Using Lattice Models by : Md Kamrul Islam
Download or read book Memetic Approach for Prediction of Low Resolution Protein Structures Using Lattice Models written by Md Kamrul Islam and published by . This book was released on 2011 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are biochemical compounds and consist essentially of linear chain of amino acids which fold quickly into a three dimensional native structure to facilitate specific biological functions. Various computational approaches, often studied to determine (in silico) protein structures, are categorised in two main categories, namely, ab initio approach (without any prior information) or the homology approach (template based). To reduce computational complexity, ab initio approaches often apply simple low resolution HP model of proteins which represent amino acids as hydrophobic (H) or hydrophilic (P), for investigating protein structure prediction (PSP) problem. In spite of this simplicity, the protein structure prediction (PSP) problem remains NP hard, emphasising the need for development of suitable evolutionary search algorithms. A memetic algorithm (MA) has the ability to perform both local and global search and also has flexible architecture. This thesis focuses on design and development of novel features for memetic search algorithm making it suitable for the complex ab initio approach for PSP studies. An energy function is developed which maintains an effective dominance of two important properties of amino acids, namely, hydrophobicity and hydrophilicity. Further, rather than a random individual generation technique, we propose an efficient technique that dynamically generates individuals. This technique is not only fast but it also ensures that the diversity of population is maintained. Moreover, highlighting the limitation of current techniques (absolute and relative) for encoding proteins, we develop a generalised non-isomorphic technique which can be applied to any lattice structure (2D or 3D lattice, FCC or triangular). The capability of MA is increased by incorporating two novel local search techniques based on mutation and pull moves. Memes, a concept similar to that proposed first by Dawkins in cultural evolution, are introduced as substructures that contain domain-specific knowledge which can be passed on to other individuals. At the core of the proposed MA design is the powerful and novel local search technique based on these memes. We also prove theoretically as to how these memes survive while continually undergoing the crossover and mutation operations. With complete meme identification, validation and transfer technique integrated within the proposed MA, the overall approach is referred to as cultural memetic algorithm (CMA). Not only is the PSP problem NP hard, it is also a complex multimodal problem. As all EAs have the tendency to get trapped into local minima due to genetic drift, techniques are necessary to surmount this difficulty. We propose a novel scalable niching technique, called Divide-and-Conquer Niching (DCN), that preserves and utilises the global domain information from multiple peaks (i.e., basins of attraction) and guides the search quickly to the "best" basin of attraction. Since the proposed niching technique is scalable in nature, we have developed a suitable architecture to enable running the DCN in parallel on a cluster. To cope with the complexity posed by long protein sequences, two effective techniques for mutation and crossover are developed, namely, conflict-resolution-based-crossover and conflict-resolution-based-mutation. Both the techniques resolve overlapping of the sequence with minimum possible changes. These techniques are deployed within the DCN on CMA to speed up convergence for long protein sequences. Experimental results show that DCN on CMA achieves optimum energy for various benchmark sequences studied on four widely used lattice models (i.e., 2D square, 3D cubic, 2D triangular and 3D FCC) and performs more reliably compared to major state of the art algorithms.
Book Synopsis Intelligent Computing Theories and Application by : De-Shuang Huang
Download or read book Intelligent Computing Theories and Application written by De-Shuang Huang and published by Springer. This book was released on 2016-07-11 with total page 882 pages. Available in PDF, EPUB and Kindle. Book excerpt: This two-volume set LNCS 9771 and LNCS 9772 constitutes - in conjunction with the volume LNAI 9773 - the refereed proceedings of the 12th International Conference on Intelligent Computing, ICIC 2016, held in Lanzhou, China, in August 2016. The 221 full papers and 15 short papers of the three proceedings volumes were carefully reviewed and selected from 639 submissions. The papers are organized in topical sections such as signal processing and image processing; information security, knowledge discovery, and data mining; systems biology and intelligent computing in computational biology; intelligent computing in scheduling; information security; advances in swarm intelligence: algorithms and applications; machine learning and data analysis for medical and engineering applications; evolutionary computation and learning; independent component analysis; compressed sensing, sparse coding; social computing; neural networks; nature inspired computing and optimization; genetic algorithms; signal processing; pattern recognition; biometrics recognition; image processing; information security; virtual reality and human-computer interaction; healthcare informatics theory and methods; artificial bee colony algorithms; differential evolution; memetic algorithms; swarm intelligence and optimization; soft computing; protein structure and function prediction; advances in swarm intelligence: algorithms and applications; optimization, neural network, and signal processing; biomedical informatics and image processing; machine learning; knowledge discovery and natural language processing; nature inspired computing and optimization; intelligent control and automation; intelligent data analysis and prediction; computer vision; knowledge representation and expert system; bioinformatics.
Book Synopsis Genetic Algorithm for Ab Initio Protein Structure Prediction Based on Low Resolution Models by : Md Tamjidul Hoque
Download or read book Genetic Algorithm for Ab Initio Protein Structure Prediction Based on Low Resolution Models written by Md Tamjidul Hoque and published by . This book was released on 2007 with total page 466 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 Biomedical Data and Applications by : Amandeep S. Sidhu
Download or read book Biomedical Data and Applications written by Amandeep S. Sidhu and published by Springer Science & Business Media. This book was released on 2009-06-16 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Compared with data from general application domains, modern biological data has many unique characteristics. The goal of this book is to cover data and applications identifying new issues and directions for future research in biomedical domain.
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 Solving the Protein Structure Prediction Problem with Fast Messy Genetic Algorithms (Scaling the Fast Messy Genetic Algorithm to Medium-Sized Peptides by Detecting Secondary Structures) by : Steven R. Michaud
Download or read book Solving the Protein Structure Prediction Problem with Fast Messy Genetic Algorithms (Scaling the Fast Messy Genetic Algorithm to Medium-Sized Peptides by Detecting Secondary Structures) written by Steven R. Michaud and published by . This book was released on 2001-03-01 with total page 259 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability to accurately predict a polypeptide's molecular structure given its amino acid sequence is important to numerous scientific, medical, and engineering applications. Studies have been conducted in the application of Genetic Algorithms (GAs) to this problem with promising initial results. In this thesis report, we use the fast messy Genetic Algorithm (fmGA) to attempt to find the minimization of an empirical CHARMM energy model and generation of the associated conformation. Previous work has shown that the fmGA provided favorable results, at least when applied to the pentapeptide Met-Enkephalin. We extend these results to a larger Polyalinine peptide by utilizing secondary structure information as both searching constraints and seeding the initial population. Additional efforts where conducted to improve the performance of the algorithm with respect to solving the Protein Structure Prediction (PSP) problem through a short-circuiting operator--where complete evaluation of the fitness function is halted if initial results are not promising, and by conducting additional searches on faster machines in a heterogeneous environment. Results indicate that, on average, this localized search tends to produce better final solutions. Finally, the fmGA as applied to the PSP problem is analyzed and shown to have improved performance and effectiveness.
Book Synopsis Nature-inspired Methods in Chemometrics: Genetic Algorithms and Artificial Neural Networks by : Riccardo Leardi
Download or read book Nature-inspired Methods in Chemometrics: Genetic Algorithms and Artificial Neural Networks written by Riccardo Leardi and published by Elsevier. This book was released on 2003-12-03 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years Genetic Algorithms (GA) and Artificial Neural Networks (ANN) have progressively increased in importance amongst the techniques routinely used in chemometrics. This book contains contributions from experts in the field is divided in two sections (GA and ANN). In each part, tutorial chapters are included in which the theoretical bases of each technique are expertly (but simply) described. These are followed by application chapters in which special emphasis will be given to the advantages of the application of GA or ANN to that specific problem, compared to classical techniques, and to the risks connected with its misuse. This book is of use to all those who are using or are interested in GA and ANN. Beginners can focus their attentions on the tutorials, whilst the most advanced readers will be more interested in looking at the applications of the techniques. It is also suitable as a reference book for students. Subject matter is steadily increasing in importance Comparison of Genetic Algorithms (GA) and Artificial Neural Networks (ANN) with the classical techniques Suitable for both beginners and advanced researchers
Book Synopsis Prediction of Protein Structures, Functions, and Interactions by : Janusz M. Bujnicki
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.
Book Synopsis Encyclopedia of Bioinformatics and Computational Biology by :
Download or read book Encyclopedia of Bioinformatics and Computational Biology written by and published by Elsevier. This book was released on 2018-08-21 with total page 3421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases
Book Synopsis Multi-Agent-Based Simulations Applied to Biological and Environmental Systems by : Adamatti, Diana Francisca
Download or read book Multi-Agent-Based Simulations Applied to Biological and Environmental Systems written by Adamatti, Diana Francisca and published by IGI Global. This book was released on 2016-12-12 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: The discovery and development of new computational methods have expanded the capabilities and uses of simulations. With agent-based models, the applications of computer simulations are significantly enhanced. Multi-Agent-Based Simulations Applied to Biological and Environmental Systems is a pivotal reference source for the latest research on the implementation of autonomous agents in computer simulation paradigms. Featuring extensive coverage on relevant applications, such as biodiversity conservation, pollution reduction, and environmental risk assessment, this publication is an ideal source for researchers, academics, engineers, practitioners, and professionals seeking material on various issues surrounding the use of agent-based simulations.
Book Synopsis Search Algorithms and Applications by : Nashat Mansour
Download or read book Search Algorithms and Applications written by Nashat Mansour and published by IntechOpen. This book was released on 2011-04-26 with total page 506 pages. Available in PDF, EPUB and Kindle. Book excerpt: Search algorithms aim to find solutions or objects with specified properties and constraints in a large solution search space or among a collection of objects. A solution can be a set of value assignments to variables that will satisfy the constraints or a sub-structure of a given discrete structure. In addition, there are search algorithms, mostly probabilistic, that are designed for the prospective quantum computer. This book demonstrates the wide applicability of search algorithms for the purpose of developing useful and practical solutions to problems that arise in a variety of problem domains. Although it is targeted to a wide group of readers: researchers, graduate students, and practitioners, it does not offer an exhaustive coverage of search algorithms and applications. The chapters are organized into three parts: Population-based and quantum search algorithms, Search algorithms for image and video processing, and Search algorithms for engineering applications.
Book Synopsis Genetic Algorithm for Ab Initio Protein Structure Prediction by : Hoque Tamjidul
Download or read book Genetic Algorithm for Ab Initio Protein Structure Prediction written by Hoque Tamjidul and published by LAP Lambert Academic Publishing. This book was released on 2013 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein is a sequence of amino acids bounded into a linear chain that adopts a specific folded three-dimensional (3D) shape. This specific folded shape enables protein to perform specific tasks. Amongst various available computational methods, the protein structure prediction by the ab initio approach is promising and can help to unravel the relationship between sequence and its associated structure. This book is focused on the ab initio protein structure prediction (PSP), by developing novel Genetic Algorithm (GA) for an efficient and effective conformation search of low resolution models. The book also proposes a novel low resolution model, called hHPNX model providing more accurate predictions compared to the existing low resolution HP models. Extensions of these developed algorithms are very promising for high resolution models.
Author :Management Association, Information Resources Publisher :IGI Global ISBN 13 :152258904X Total Pages :2183 pages Book Rating :4.5/5 (225 download)
Book Synopsis Biotechnology: Concepts, Methodologies, Tools, and Applications by : Management Association, Information Resources
Download or read book Biotechnology: Concepts, Methodologies, Tools, and Applications written by Management Association, Information Resources and published by IGI Global. This book was released on 2019-06-07 with total page 2183 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biotechnology can be defined as the manipulation of biological process, systems, and organisms in the production of various products. With applications in a number of fields such as biomedical, chemical, mechanical, and civil engineering, research on the development of biologically inspired materials is essential to further advancement. Biotechnology: Concepts, Methodologies, Tools, and Applications is a vital reference source for the latest research findings on the application of biotechnology in medicine, engineering, agriculture, food production, and other areas. It also examines the economic impacts of biotechnology use. Highlighting a range of topics such as pharmacogenomics, biomedical engineering, and bioinformatics, this multi-volume book is ideally designed for engineers, pharmacists, medical professionals, practitioners, academicians, and researchers interested in the applications of biotechnology.
Book Synopsis The Monte Carlo Approach To Biopolymers And Protein Folding by : Peter Grassberger
Download or read book The Monte Carlo Approach To Biopolymers And Protein Folding written by Peter Grassberger and published by World Scientific. This book was released on 1998-11-06 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: Information on our detailed genetic code is increasing at a dramatic pace. We need to understand how that is translated into the three-dimensional structure of proteins in order to make use of the information. Progress in this field is hampered by the lack of precise force fields and of efficient codes for finding equilibrium configurations of heteropolymers. However, there has been rapid advance in recent years, and this volume discusses that.
Book Synopsis Algorithms and Architectures for Parallel Processing, Part II by : Yang Xiang
Download or read book Algorithms and Architectures for Parallel Processing, Part II written by Yang Xiang and published by Springer. This book was released on 2011-10-23 with total page 431 pages. Available in PDF, EPUB and Kindle. Book excerpt: This two volume set LNCS 7016 and LNCS 7017 constitutes the refereed proceedings of the 11th International Conference on Algorithms and Architectures for Parallel Processing, ICA3PP 2011, held in Melbourne, Australia, in October 2011. The second volume includes 37 papers from one symposium and three workshops held together with ICA3PP 2011 main conference. These are 16 papers from the 2011 International Symposium on Advances of Distributed Computing and Networking (ADCN 2011), 10 papers of the 4th IEEE International Workshop on Internet and Distributed Computing Systems (IDCS 2011), 7 papers belonging to the III International Workshop on Multicore and Multithreaded Architectures and Algorithms (M2A2 2011), as well as 4 papers of the 1st IEEE International Workshop on Parallel Architectures for Bioinformatics Systems (HardBio 2011).