Download or read book Local Search based Protein Folding Simulations written by Leonidas Kapsokalyvas and published by . This book was released on 2011 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract. Protein folding is the physical process in which a protein acquires its structure that allows it to perform a specific biological task. Proteins fold spon-taneously into three-dimensional structures of minimum energy when found in the appropriate environment. The study of this phenomenon is often facilitated through local search-based computer simulations in which the energy of a protein is mini¬mized. This thesis is concerned with local search methods for protein folding simulations in rectangular and triangular lattice models as well as in a simplified coarse-grained off-lattice model. The aim of those simulations is on the one hand protein struc¬ture prediction and on the other hand energy landscape analysis. Lattice models are often useful in the study of protein folding, since they allow exact enumeration of solutions, easy identification of local minima and paths leading to them. The challenge for local search-based methods in lattice model simulations is to efficiently sample an exponentially large search space. In that respect this thesis contributes a method to reduce the search space in rectangular lattices, which is adapted into specific neighborhood relations and is used in local search methods. This method is based on restricting search to a reduced subspace of protein structures, free from some special symmetrical versions of the same structure. The thesis also contributes a novel local search method for protein structure prediction, namely a population based local search. The novel local search method can be used to gather local min¬ima of the underlying energy landscape. The method outperforms the state-of-the-art method tested for the specific set of benchmarks in the cubic lattice and the MJ(Miyazawa-Jernigan) energy model. The survey of the energy landscape in the latter model reveals that the energy of local minima follows a Gaussian-like distri¬bution.
Download or read book Bioinformatics Research and Development written by Mourad Elloumi and published by Springer Science & Business Media. This book was released on 2008-08-31 with total page 613 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains the papers which were selected for presentation at the second Bio- formatics Research and Development (BIRD) conference held in Vienna, Austria during July 7–9, 2008. BIRD covers a wide range of topics related to bioinformatics. This year sequence analysis and alignment, pathways, networks, systems biology, protein and RNA structure and function, gene expression/regulation and microarrays, databases and data integration, machine learning and data analysis were the subjects of main interest. The decisions of the Program Committee are based on the recommendations of at least three, up to five, reviews for each paper. As a result, 30 of the 61 submitted c- tributions could be accepted for the conference. We were happy to have three invited talks presented by experienced researchers providing visitors with a good overview but also some very important insights into the fascinating domain of bioinformatics. Abstracts and more information on these talks are provided in the conference program as well as at the conference site. In the second part of this volume the selected contributions of the two workshops which were held in parallel to the main conference are presented: Workshop on - namical Aspects of Perturbation, Intervention and Transition in Biological Systems – PETRIN 2008 and Workshop on Algorithms in Molecular Biology – ALBIO 2008 Poster presentations of the BIRD conference are in the companion proceedings published by the Trauner Verlag, Linz.
Download or read book Bioinformatics Research and Development written by Sepp Hochreiter and published by Springer. This book was released on 2007-05-21 with total page 497 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the First International Bioinformatics Research and Development Conference, BIRD 2007, held in Berlin, Germany in March 2007. The 36 revised full papers are organized in topical sections on microarray and systems biology and networks, medical, SNPs, genomics, systems biology, sequence analysis and coding, proteomics and structure, databases, Web and text analysis.
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.
Download or read book The Protein Folding Problem and Tertiary Structure Prediction written by Kenneth M. Merz and published by . This book was released on 1994-01-01 with total page 581 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Intelligence and Intelligent Systems written by Zhenhua Li and published by Springer. This book was released on 2009-11-03 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volumes CCIS 51 and LNCS 5812 constitute the proceedings of the Fourth Interational Symposium on Intelligence Computation and Applications, ISICA 2009, held in Huangshi, China, during October 23-25. ISICA 2009 attracted over 300 submissions. Through rigorous reviews, 58 papers were included in LNCS 5821, and 54 papers were collected in CCIS 51. ISICA conferences are one of the first series of international conferences on computational intelligence that combine elements of learning, adaptation, evolution and fuzzy logic to create programs as alternative solutions to artificial intelligence.
Download or read book Constrained Optimization and Lagrange Multiplier Methods written by Dimitri P. Bertsekas and published by Academic Press. This book was released on 2014-05-10 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computer Science and Applied Mathematics: Constrained Optimization and Lagrange Multiplier Methods focuses on the advancements in the applications of the Lagrange multiplier methods for constrained minimization. The publication first offers information on the method of multipliers for equality constrained problems and the method of multipliers for inequality constrained and nondifferentiable optimization problems. Discussions focus on approximation procedures for nondifferentiable and ill-conditioned optimization problems; asymptotically exact minimization in the methods of multipliers; duality framework for the method of multipliers; and the quadratic penalty function method. The text then examines exact penalty methods, including nondifferentiable exact penalty functions; linearization algorithms based on nondifferentiable exact penalty functions; differentiable exact penalty functions; and local and global convergence of Lagrangian methods. The book ponders on the nonquadratic penalty functions of convex programming. Topics include large scale separable integer programming problems and the exponential method of multipliers; classes of penalty functions and corresponding methods of multipliers; and convergence analysis of multiplier methods. The text is a valuable reference for mathematicians and researchers interested in the Lagrange multiplier methods.
Download or read book Advances in Artificial Intelligence written by Yang Xiang and published by Springer. This book was released on 2003-08-03 with total page 656 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 16th Conference of the Canadian Society for Computational Studies of Intelligence, AI 2003, held in Halifax, Canada in June 2003. The 30 revised full papers and 24 revised short papers presented were carefully reviewed and selected from 106 submissions. The papers are organized in topical sections on knowledge representation, search, constraint satisfaction, machine learning and data mining, AI and Web applications, reasoning under uncertainty, agents and multi-agent systems, AI and bioinformatics, and AI and e-commerce.
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.
Download or read book Learning and Intelligent Optimization written by Christian Blum and published by Springer Science & Business Media. This book was released on 2010-07-07 with total page 357 pages. Available in PDF, EPUB and Kindle. Book excerpt: The LNCS series reports state-of-the-art results in computer science research, development, and education, at a high level and in both printed and electronic form. Enjoying tight cooperation with the R&D community, with numerous individuals, as well as with prestigious organizations and societies, LNCS has grown into the most comprehensive computer science research forum available. The scope of LNCS, including its subseries LNAI and LNBI, spans the whole range of computer science and information technology including interdisciplinary topics in a variety of application fields. In parallel to the printed book, each new volume is published electronically in LNCS Online.
Download or read book PRICAI 2014 Trends in Artificial Intelligence written by Duc-Nghia Pham and published by Springer. This book was released on 2014-11-12 with total page 1122 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 13th Pacific Rim Conference on Artificial Intelligence, PRICAI 2014, held in Gold Coast, Queensland, Australia, in December 2014. The 74 full papers and 20 short papers presented in this volume were carefully reviewed and selected from 203 submissions. The topics include inference; reasoning; robotics; social intelligence. AI foundations; applications of AI; agents; Bayesian networks; neural networks; Markov networks; bioinformatics; cognitive systems; constraint satisfaction; data mining and knowledge discovery; decision theory; evolutionary computation; games and interactive entertainment; heuristics; knowledge acquisition and ontology; knowledge representation, machine learning; multimodal interaction; natural language processing; planning and scheduling; probabilistic.
Download or read book Protein Folding Dynamics Using Multi scale Computational Methods written by Taisong Zou and published by . This book was released on 2014 with total page 144 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis explores a wide array of topics related to the protein folding problem, ranging from the folding mechanism, ab initio structure prediction and protein design, to the mechanism of protein functional evolution, using multi-scale approaches. To investigate the role of native topology on folding mechanism, the native topology is dissected into non-local and local contacts. The number of non-local contacts and non-local contact orders are both negatively correlated with folding rates, suggesting that the non-local contacts dominate the barrier-crossing process. However, local contact orders show positive correlation with folding rates, indicating the role of a diffusive search in the denatured basin. Additionally, the folding rate distribution of E. coli and Yeast proteomes are predicted from native topology. The distribution is fitted well by a diffusion-drift population model and also directly compared with experimentally measured half life. The results indicate that proteome folding kinetics is limited by protein half life. The crucial role of local contacts in protein folding is further explored by the simulations of WW domains using Zipping and Assembly Method. The correct formation of N-terminal & beta;-turn turns out important for the folding of WW domains. A classification model based on contact probabilities of five critical local contacts is constructed to predict the foldability of WW domains with 81% accuracy. By introducing mutations to stabilize those critical local contacts, a new protein design approach is developed to re-design the unfoldable WW domains and make them foldable. After folding, proteins exhibit inherent conformational dynamics to be functional. Using molecular dynamics simulations in conjunction with Perturbation Response Scanning, it is demonstrated that the divergence of functions can occur through the modification of conformational dynamics within existing fold for & beta;-lactmases and GFP-like proteins: i) the modern TEM-1 lactamase shows a comparatively rigid active-site region, likely reflecting adaptation for efficient degradation of a specific substrate, while the resurrected ancient lactamases indicate enhanced active-site flexibility, which likely allows for the binding and subsequent degradation of different antibiotic molecules; ii) the chromophore and attached peptides of photocoversion-competent GFP-like protein exhibits higher flexibility than the photocoversion-incompetent one, consistent with the evolution of photocoversion capacity.
Download or read book Evolutionary Computation Machine Learning and Data Mining in Bioinformatics written by Clara Pizzuti and published by Springer. This book was released on 2010-04-03 with total page 259 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 7th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, EvoBIO 2010, held in Istanbul, Turkey, in April 2010 co-located with the Evo* 2010 events. This 15 revised full papers were carefully reviewed and selected from 40 submissions. EvoBIO is the premiere European event for those interested in the interface between evolutionary computation, machine learning, data mining, bioinformatics, and computational biology. Topics addressed by the papers include biomarker discovery, cell simulation and modeling, ecological modeling, fluxomics, gene networks, biotechnology, metabolomics, microarray analysis, phylogenetics, protein interactions, proteomics, sequence analysis and alignment, and systems biology.
Download or read book AI 2013 Advances in Artificial Intelligence written by Stephen Cranefield and published by Springer. This book was released on 2013-11-08 with total page 534 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 26th Australasian Joint Conference on Artificial Intelligence, AI 2013, held in Dunedin, New Zealand, in December 2013. The 35 revised full papers and 19 revised short papers presented were carefully reviewed and selected from 120 submissions. The papers are organized in topical sections as agents; AI applications; cognitive modelling; computer vision; constraint satisfaction, search and optimisation; evolutionary computation; game playing; knowledge representation and reasoning; machine learning and data mining; natural language processing and information retrieval; planning and scheduling.
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.
Download or read book Principles and Practice of Constraint Programming written by Peter J. Stuckey and published by Springer Science & Business Media. This book was released on 2008-08-28 with total page 662 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains the proceedings of the 14th International Conference on Principles and Practice of Constraint Programming (CP 2008) held in Sydney, Australia, September 14–18, 2008. The conference was held in conjunction with the International Conference on Automated Planning and Scheduling (ICAPS 2008) and the International Conference on Knowledge Representation and R- soning (KR 2008). Information about the conference can be found at the w- sitehttp://www. unimelb. edu. au/cp2008/. Held annually, the CP conference series is the premier international conference on constraint programming. The conference focuses on all aspects of computing with constraints. The CP conf- ence series is organized by the Association for Constraint Programming (ACP). Information about the conferences in the series can be found on the Web at http://www. cs. ualberta. ca/~ai/cp/. Information about ACP can be found athttp://www. a4cp. org/. CP 2008 included two calls for contributions: a call for research papers, - scribing novel contributions in the ?eld, and a call for application papers, - scribing applications of constraint technology. For the ?rst time authors could directly submit short papers for consideration by the committee. The research track received 84 long submissions and 21 short submissions and the application track received 15 long submissions. Each paper received at least three reviews, which the authors had the opportunity to see and to react to, before the papers and their reviews were discussed extensively by the members of the Program Committee.
