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Genetic Algorithm For Ab Initio Protein Structure Prediction Based On Low Resolution Models
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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 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.
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 Bioinformatics and Computational Biology by : Tiratha Raj Singh
Download or read book Bioinformatics and Computational Biology written by Tiratha Raj Singh and published by CRC Press. This book was released on 2023-12-13 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics and Computational Biology: Technological Advancements, Applications and Opportunities is an invaluable resource for general and applied researchers who analyze biological data that is generated, at an unprecedented rate, at the global level. After careful evaluation of the requirements for current trends in bioinformatics and computational biology, it is anticipated that the book will provide an insightful resource to the academic and scientific community. Through a myriad of computational resources, algorithms, and methods, it equips readers with the confidence to both analyze biological data and estimate predictions. The book offers comprehensive coverage of the most essential and emerging topics: Cloud-based monitoring of bioinformatics multivariate data with cloud platforms Machine learning and deep learning in bioinformatics Quantum machine learning for biological applications Integrating machine learning strategies with multiomics to augment prognosis in chronic diseases Biomedical engineering Next generation sequencing techniques and applications Computational systems biology and molecular evolution While other books may touch on some of the same issues and nuances of biological data analysis, they neglect to feature bioinformatics and computational biology exclusively, and as exhaustively. This book's abundance of several subtopics related to almost all of the regulatory activities of biomolecules from where real data is being generated brings an added dimension.
Book Synopsis AI 2012: Advances in Artificial Intelligence by : Michael Thielscher
Download or read book AI 2012: Advances in Artificial Intelligence written by Michael Thielscher and published by Springer. This book was released on 2013-02-01 with total page 935 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 25th Australasian Joint Conference on Artificial Intelligence, AI 2012, held in Sydney, Australia, in December 2012. The 76 revised full papers presented were carefully reviewed and selected from 196 submissions. The papers address a wide range of agents, applications, computer vision, constraints and search, game playing, information retrieval, knowledge representation, machine learning, planning and scheduling, robotics and uncertainty in AI.
Book Synopsis Proceedings of Fifth International Conference on Soft Computing for Problem Solving by : Millie Pant
Download or read book Proceedings of Fifth International Conference on Soft Computing for Problem Solving written by Millie Pant and published by Springer. This book was released on 2016-04-20 with total page 1021 pages. Available in PDF, EPUB and Kindle. Book excerpt: The proceedings of SocProS 2015 will serve as an academic bonanza for scientists and researchers working in the field of Soft Computing. This book contains theoretical as well as practical aspects using fuzzy logic, neural networks, evolutionary algorithms, swarm intelligence algorithms, etc., with many applications under the umbrella of ‘Soft Computing’. The book will be beneficial for young as well as experienced researchers dealing across complex and intricate real world problems for which finding a solution by traditional methods is a difficult task. The different application areas covered in the proceedings are: Image Processing, Cryptanalysis, Industrial Optimization, Supply Chain Management, Newly Proposed Nature Inspired Algorithms, Signal Processing, Problems related to Medical and Health Care, Networking Optimization Problems, etc.
Book Synopsis Global Virology III: Virology in the 21st Century by : Paul Shapshak
Download or read book Global Virology III: Virology in the 21st Century written by Paul Shapshak and published by Springer Nature. This book was released on 2019-11-22 with total page 671 pages. Available in PDF, EPUB and Kindle. Book excerpt: Global Virology, Volume III: Virology in the 21st Century examines work that has been undertaken, or is planned, in several fields of virology, in an effort to promote current and future work, research, and health. Fields and methods addressed include virology, immunology, space research, astrovirology/astrobiology, plasmids, swarm intelligence, bioinformatics, data-mining, machine learning, neural networks, critical equations, and advances in biohazard biocontainment. Novel and forward-looking methods, techniques, and approaches in research and development are presented by experts in the 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 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 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 Computational Methods in Genome Research by : Sándor Suhai
Download or read book Computational Methods in Genome Research written by Sándor Suhai and published by Springer Science & Business Media. This book was released on 1994 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chapters originating as plenary lectures at the July 1992 symposium provide a bridge between experimental databases (information) on the one hand and theoretical concepts (biological and genetic knowledge) on the other. Among the topics: informatics and experiments for the Human Genome Project; the
Book Synopsis AI 2009: Advances in Artificial Intelligence by : Ann Nicholson
Download or read book AI 2009: Advances in Artificial Intelligence written by Ann Nicholson and published by Springer Science & Business Media. This book was released on 2009-11-09 with total page 702 pages. Available in PDF, EPUB and Kindle. Book excerpt: We are pleased to present this LNCS volume, the Proceedings of the 22nd A- tralasianJointConferenceonArti?cialIntelligence(AI2009),heldinMelbourne, Australia, December 1–4,2009.This long established annual regionalconference is a forum both for the presentation of researchadvances in arti?cial intelligence and for scienti?c interchange amongst researchers and practitioners in the ?eld of arti?cial intelligence. Conference attendees were also able to enjoy AI 2009 being co-located with the Australasian Data Mining Conference (AusDM 2009) and the 4th Australian Conference on Arti?cial Life (ACAL 2009). This year AI 2009 received 174 submissions, from authors of 30 di?erent countries. After an extensive peer review process where each submitted paper was rigorously reviewed by at least 2 (and in most cases 3) independent revi- ers, the best 68 papers were selected by the senior Program Committee for oral presentation at the conference and included in this volume, resulting in an - ceptance rate of 39%. The papers included in this volume cover a wide range of topics in arti?cial intelligence: from machine learning to natural language s- tems, from knowledge representation to soft computing, from theoretical issues to real-world applications. AI 2009 also included 11 tutorials, available through the First Australian Computational Intelligence Summer School (ACISS 2009). These tutorials – some introductory, some advanced – covered a wide range of research topics within arti?cial intelligence, including data mining, games, evolutionary c- putation, swarm optimization, intelligent agents, Bayesian and belief networks.
Book Synopsis Neural Information Processing by : Bao-Liang Lu
Download or read book Neural Information Processing written by Bao-Liang Lu and published by Springer Science & Business Media. This book was released on 2011-10-26 with total page 788 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three volume set LNCS 7062, LNCS 7063, and LNCS 7064 constitutes the proceedings of the 18th International Conference on Neural Information Processing, ICONIP 2011, held in Shanghai, China, in November 2011. The 262 regular session papers presented were carefully reviewed and selected from numerous submissions. The papers of part I are organized in topical sections on perception, emotion and development, bioinformatics, biologically inspired vision and recognition, bio-medical data analysis, brain signal processing, brain-computer interfaces, brain-like systems, brain-realistic models for learning, memory and embodied cognition, Clifford algebraic neural networks, combining multiple learners, computational advances in bioinformatics, and computational-intelligent human computer interaction. The second volume is structured in topical sections on cybersecurity and data mining workshop, data mining and knowledge doscovery, evolutionary design and optimisation, graphical models, human-originated data analysis and implementation, information retrieval, integrating multiple nature-inspired approaches, kernel methods and support vector machines, and learning and memory. The third volume contains all the contributions connected with multi-agent systems, natural language processing and intelligent Web information processing, neural encoding and decoding, neural network models, neuromorphic hardware and implementations, object recognition, visual perception modelling, and advances in computational intelligence methods based pattern recognition.
Book Synopsis AB Initio Protein Tertiary Structure Prediction by :
Download or read book AB Initio Protein Tertiary Structure Prediction written by and published by . This book was released on 2001 with total page 6 pages. Available in PDF, EPUB and Kindle. Book excerpt: During the period from September 1, 1998 until September 1, 2000 I was awarded a Sloan/DOE postdoctoral fellowship to work in collaboration with Professor John Moult at the Center for Advanced Research in Biotechnology (CARB). Our research project, ''Ab Initio Protein Tertiary Structure Prediction and a Comparative Genetic algorithm'', yielded promising initial results. In short, the project is designed to predict the native fold, or native tertiary structure, of a given protein by inputting only the primary sequence of the protein (one or three letter code). The algorithm is based on a general learning, or evolutionary algorithm and is called Genetic Algorithm (GAS). In our particular application of GAS, we search for native folds, or lowest energy structures, using two different descriptions for the interactions of the atoms and residues in a given protein sequence. One potential energy function is based on a free energy description, while the other function is a threading potential derived by Moult and Samudrala. This modified genetic algorithm was loosely termed a Comparative Genetic Algorithm and was designed to search for native folded structures on both potential energy surfaces, simultaneously. We tested the algorithm on a series of peptides ranging from 11 to 15 residues in length, which are thought to be independent folding units and thereby will fold to native structures independent of the larger protein environment. Our initial results indicated a modest increase in accuracy, as compared to a standard Genetic Algorithm. We are now in the process of improving the algorithm to increase the sensitivity to other inputs, such as secondary structure requirements. The project did not involve additional students and as of yet, the work has not been published.
Book Synopsis Soft Computing Techniques in Vision Science by : Srikanta Patnaik
Download or read book Soft Computing Techniques in Vision Science written by Srikanta Patnaik and published by Springer Science & Business Media. This book was released on 2012-02-15 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: This Special Edited Volume is a unique approach towards Computational solution for the upcoming field of study called Vision Science. From a scientific firmament Optics, Ophthalmology, and Optical Science has surpassed an Odyssey of optimizing configurations of Optical systems, Surveillance Cameras and other Nano optical devices with the metaphor of Nano Science and Technology. Still these systems are falling short of its computational aspect to achieve the pinnacle of human vision system. In this edited volume much attention has been given to address the coupling issues Computational Science and Vision Studies. It is a comprehensive collection of research works addressing various related areas of Vision Science like Visual Perception and Visual system, Cognitive Psychology, Neuroscience, Psychophysics and Ophthalmology, linguistic relativity, color vision etc. This issue carries some latest developments in the form of research articles and presentations. The volume is rich of contents with technical tools for convenient experimentation in Vision Science. There are 18 research papers having significance in an array of application areas. The volume claims to be an effective compendium of computing developments like Frequent Pattern Mining, Genetic Algorithm, Gabor Filter, Support Vector Machine, Region Based Mask Filter, 4D stereo camera systems, Principal Component Analysis etc. The detailed analysis of the papers can immensely benefit to the researchers of this domain. It can be an Endeavour in the pursuit of adding value in the existing stock of knowledge in Vision Science.
Book Synopsis BIOINFORMATICS, FIFTH EDITION by : RASTOGI, S.C.
Download or read book BIOINFORMATICS, FIFTH EDITION written by RASTOGI, S.C. and published by PHI Learning Pvt. Ltd.. This book was released on 2022-04-05 with total page 624 pages. Available in PDF, EPUB and Kindle. Book excerpt: Designed as a comprehensive text for students and professionals pursuing careers in the fields of bioinformatics, molecular biology, pharmacy and drug research, the Fifth Edition continues to offer a fascinating and authoritative treatment of the entire spectrum of bioinformatics, covering a wide range of high-throughput technologies. The content can be used for four core courses: bioinformatics fundamentals, genomics, proteomics and drug discovery and design. The Fifth Edition takes a completely new pedagogical approach and the book is divided into eight distinct Units for the ease of learning: Bioinformatics Fundamentals, Sequence Alignment, Phylogenetic Analysis, Genomics, Protein Structure and Function, Drug Discovery Methods, Drug Design and Development and Integrative Topics. Accordingly, all the chapters are revised and updated in the new edition, besides introduction of seven new chapters and another seven completely re-written chapters. As a student-friendly text, it embodies several pedagogical features such as detailed examples, numerous tables, a large number of diagrams, flow charts and web resources. The book in its present edition should prove an invaluable asset to the students and researchers in the fields of bioinformatics, biotechnology, computer-aided drug design, information technology, medical diagnostics, molecular biology and pharmaceutical sciences. NEW TO THE FIFTH EDITION • Re-written chapters — Biological database search and data retrieval, Pair-wise alignment of sequences, PSSMs and Hidden Markov Models, Gene Mapping, Gene Prediction, Protein Structure Overview and Protein Structure Prediction. • Inclusion of new chapters—Scoring Matrices, Gene Sequencing, Regulatory Elements Prediction, Comparative Genomics, Protein Structure Databases, Protein Function Prediction and Potential Drug Targets. KEY FEATURES • Covers the field of bioinformatics in a complete and integrated approach – moving from the fundamentals to theory and practical applications. • State-of-the-art technologies for gene identification, molecular modeling and monitoring of cellular processes. • Data mining, data curation and analysis, classification, interpretation and efficient structure determination of genomes and proteomes. • Companion website provides useful resources for the teachers as well as for the students. So, visit Learning Centre https:// www.phindia.com/bioinformatics_mendiratta_rastogi to have access of Lecture notes, solutions manual, MCQs, problems set for practice, glossary of important terms, etc. TARGET AUDIENCE • UG and PG Students of Bioinformatics, Biotechnology, Molecular Biology and Pharmacy.
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.
