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Book Protein Structure Prediction

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 Prediction of Protein Structures  Functions  and Interactions

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 Protein Structure Prediction and Gene Bi clustering by Soft Computing Approach

Download or read book Protein Structure Prediction and Gene Bi clustering by Soft Computing Approach written by Dr Veera Talukdar and published by Archers & Elevators Publishing House. This book was released on with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Book A Metaheuristic Approach to Protein Structure Prediction

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 Machine Learning Meets Quantum Physics

Download or read book Machine Learning Meets Quantum Physics written by Kristof T. Schütt and published by Springer Nature. This book was released on 2020-06-03 with total page 473 pages. Available in PDF, EPUB and Kindle. Book excerpt: Designing molecules and materials with desired properties is an important prerequisite for advancing technology in our modern societies. This requires both the ability to calculate accurate microscopic properties, such as energies, forces and electrostatic multipoles of specific configurations, as well as efficient sampling of potential energy surfaces to obtain corresponding macroscopic properties. Tools that can provide this are accurate first-principles calculations rooted in quantum mechanics, and statistical mechanics, respectively. Unfortunately, they come at a high computational cost that prohibits calculations for large systems and long time-scales, thus presenting a severe bottleneck both for searching the vast chemical compound space and the stupendously many dynamical configurations that a molecule can assume. To overcome this challenge, recently there have been increased efforts to accelerate quantum simulations with machine learning (ML). This emerging interdisciplinary community encompasses chemists, material scientists, physicists, mathematicians and computer scientists, joining forces to contribute to the exciting hot topic of progressing machine learning and AI for molecules and materials. The book that has emerged from a series of workshops provides a snapshot of this rapidly developing field. It contains tutorial material explaining the relevant foundations needed in chemistry, physics as well as machine learning to give an easy starting point for interested readers. In addition, a number of research papers defining the current state-of-the-art are included. The book has five parts (Fundamentals, Incorporating Prior Knowledge, Deep Learning of Atomistic Representations, Atomistic Simulations and Discovery and Design), each prefaced by editorial commentary that puts the respective parts into a broader scientific context.

Book From Protein Structure to Function with Bioinformatics

Download or read book From Protein Structure to Function with Bioinformatics written by Daniel John Rigden and published by Springer Science & Business Media. This book was released on 2008-12-11 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins lie at the heart of almost all biological processes and have an incredibly wide range of activities. Central to the function of all proteins is their ability to adopt, stably or sometimes transiently, structures that allow for interaction with other molecules. An understanding of the structure of a protein can therefore lead us to a much improved picture of its molecular function. This realisation has been a prime motivation of recent Structural Genomics projects, involving large-scale experimental determination of protein structures, often those of proteins about which little is known of function. These initiatives have, in turn, stimulated the massive development of novel methods for prediction of protein function from structure. Since model structures may also take advantage of new function prediction algorithms, the first part of the book deals with the various ways in which protein structures may be predicted or inferred, including specific treatment of membrane and intrinsically disordered proteins. A detailed consideration of current structure-based function prediction methodologies forms the second part of this book, which concludes with two chapters, focusing specifically on case studies, designed to illustrate the real-world application of these methods. With bang up-to-date texts from world experts, and abundant links to publicly available resources, this book will be invaluable to anyone who studies proteins and the endlessly fascinating relationship between their structure and function.

Book Optimization for Chemical and Biochemical Engineering

Download or read book Optimization for Chemical and Biochemical Engineering written by Vassilios S. Vassiliadis and published by Cambridge University Press. This book was released on 2021-01-14 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discover the subject of optimization in a new light with this modern and unique treatment. Includes a thorough exposition of applications and algorithms in sufficient detail for practical use, while providing you with all the necessary background in a self-contained manner. Features a deeper consideration of optimal control, global optimization, optimization under uncertainty, multiobjective optimization, mixed-integer programming and model predictive control. Presents a complete coverage of formulations and instances in modelling where optimization can be applied for quantitative decision-making. As a thorough grounding to the subject, covering everything from basic to advanced concepts and addressing real-life problems faced by modern industry, this is a perfect tool for advanced undergraduate and graduate courses in chemical and biochemical engineering.

Book Comprehensive Biophysics

Download or read book Comprehensive Biophysics written by and published by Academic Press. This book was released on 2012-04-12 with total page 3533 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biophysics is a rapidly-evolving interdisciplinary science that applies theories and methods of the physical sciences to questions of biology. Biophysics encompasses many disciplines, including physics, chemistry, mathematics, biology, biochemistry, medicine, pharmacology, physiology, and neuroscience, and it is essential that scientists working in these varied fields are able to understand each other's research. Comprehensive Biophysics, Nine Volume Set will help bridge that communication gap. Written by a team of researchers at the forefront of their respective fields, under the guidance of Chief Editor Edward Egelman, Comprehensive Biophysics, Nine Volume Set provides definitive introductions to a broad array of topics, uniting different areas of biophysics research - from the physical techniques for studying macromolecular structure to protein folding, muscle and molecular motors, cell biophysics, bioenergetics and more. The result is this comprehensive scientific resource - a valuable tool both for helping researchers come to grips quickly with material from related biophysics fields outside their areas of expertise, and for reinforcing their existing knowledge. Biophysical research today encompasses many areas of biology. These studies do not necessarily share a unique identifying factor. This work unites the different areas of research and allows users, regardless of their background, to navigate through the most essential concepts with ease, saving them time and vastly improving their understanding The field of biophysics counts several journals that are directly and indirectly concerned with the field. There is no reference work that encompasses the entire field and unites the different areas of research through deep foundational reviews. Comprehensive Biophysics fills this vacuum, being a definitive work on biophysics. It will help users apply context to the diverse journal literature offering, and aid them in identifying areas for further research Chief Editor Edward Egelman (E-I-C, Biophysical Journal) has assembled an impressive, world-class team of Volume Editors and Contributing Authors. Each chapter has been painstakingly reviewed and checked for consistent high quality. The result is an authoritative overview which ties the literature together and provides the user with a reliable background information and citation resource

Book Protein Structure Determination

Download or read book Protein Structure Determination written by Clarence H. Suelter and published by John Wiley & Sons. This book was released on 2009-09-25 with total page 310 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents methods for determining the secondary and tertiary structure of proteins. The issues covered here involve theoretical/empirical approaches for predicting protein structure; a review using protein ligand interactions to study surface properties of proteins; use of fluorescence techniques to study structure and dynamics of proteins; and limited proteolysis with monoclonal antibodies to understand how specific structural features confer biological function.

Book Pacific Symposium on Biocomputing 2003

Download or read book Pacific Symposium on Biocomputing 2003 written by Russ B. Altman and published by World Scientific. This book was released on 2002 with total page 671 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Pacific Symposium on Biocomputing (PSB 2003) is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. The rigorously peer-reviewed papers and presentations are collected in this archival proceedings volume. PSB 2003 brings together top researchers from the US, the Asia-Pacific region and around the world to exchange research findings and address open issues in all aspects of computational biology. PSB is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.

Book From Protein Structure to Function with Bioinformatics

Download or read book From Protein Structure to Function with Bioinformatics written by Daniel J. Rigden and published by Springer. This book was released on 2017-04-06 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is about protein structural bioinformatics and how it can help understand and predict protein function. It covers structure-based methods that can assign and explain protein function based on overall folds, characteristics of protein surfaces, occurrence of small 3D motifs, protein-protein interactions and on dynamic properties. Such methods help extract maximum value from new experimental structures, but can often be applied to protein models. The book also, therefore, provides comprehensive coverage of methods for predicting or inferring protein structure, covering all structural classes from globular proteins and their membrane-resident counterparts to amyloid structures and intrinsically disordered proteins. The book is split into two broad sections, the first covering methods to generate or infer protein structure, the second dealing with structure-based function annotation. Each chapter is written by world experts in the field. The first section covers methods ranging from traditional homology modelling and fold recognition to fragment-based ab initio methods, and includes a chapter, new for the second edition, on structure prediction using evolutionary covariance. Membrane proteins and intrinsically disordered proteins are each assigned chapters, while two new chapters deal with amyloid structures and means to predict modes of protein-protein interaction. The second section includes chapters covering functional diversity within protein folds and means to assign function based on surface properties and recurring motifs. Further chapters cover the key roles of protein dynamics in protein function and use of automated servers for function inference. The book concludes with two chapters covering case studies of structure prediction, based respectively on crystal structures and protein models, providing numerous examples of real-world usage of the methods mentioned previously. This book is targeted at postgraduate students and academic researchers. It is most obviously of interest to protein bioinformaticians and structural biologists, but should also serve as a guide to biologists more broadly by highlighting the insights that structural bioinformatics can provide into proteins of their interest.

Book Computational Methods for Protein Structure Prediction and Modeling

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 Computational Modeling and Simulation in Biomedical Research

Download or read book Computational Modeling and Simulation in Biomedical Research written by Yee Siew Choong and published by Bentham Science Publishers. This book was released on 2024-08-01 with total page 159 pages. Available in PDF, EPUB and Kindle. Book excerpt: This reference provides a comprehensive overview of computational modelling and simulation for theoretical and practical biomedical research. The book explains basic concepts of computational biology and data modelling for learners and early career researchers. Chapters cover these topics: 1. An introduction to computational tools in biomedical research 2. Computational analysis of biological data 3. Algorithm development for computational modelling and simulation 4. The roles and application of protein modelling in biomedical research 5. Dynamics of biomolecular ligand recognition Key features include a simple, easy-to-understand presentation, detailed explanation of important concepts in computational modeling and simulations and references.

Book Encyclopedia of Optimization

Download or read book Encyclopedia of Optimization written by Christodoulos A. Floudas and published by Springer Science & Business Media. This book was released on 2008-09-04 with total page 4646 pages. Available in PDF, EPUB and Kindle. Book excerpt: The goal of the Encyclopedia of Optimization is to introduce the reader to a complete set of topics that show the spectrum of research, the richness of ideas, and the breadth of applications that has come from this field. The second edition builds on the success of the former edition with more than 150 completely new entries, designed to ensure that the reference addresses recent areas where optimization theories and techniques have advanced. Particularly heavy attention resulted in health science and transportation, with entries such as "Algorithms for Genomics", "Optimization and Radiotherapy Treatment Design", and "Crew Scheduling".

Book Computational Methods for Protein Folding  Volume 120

Download or read book Computational Methods for Protein Folding Volume 120 written by Richard A. Friesner and published by John Wiley & Sons. This book was released on 2004-04-07 with total page 544 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the first attempts to model proteins on a computer began almost thirty years ago, our understanding of protein structure and dynamics has dramatically increased. Spectroscopic measurement techniques continue to improve in resolution and sensitivity, allowing a wealth of information to be obtained with regard to the kinetics of protein folding and unfolding, and complementing the detailed structural picture of the folded state. Concurrently, algorithms, software, and computational hardware have progressed to the point where both structural and kinetic problems may be studied with a fair degree of realism. Despite these advances, many major challenges remain in understanding protein folding at both the conceptual and practical levels. Computational Methods for Protein Folding seeks to illuminate recent advances in computational modeling of protein folding in a way that will be useful to physicists, chemists, and chemical physicists. Covering a broad spectrum of computational methods and practices culled from a variety of research fields, the editors present a full range of models that, together, provide a thorough and current description of all aspects of protein folding. A valuable resource for both students and professionals in the field, the book will be of value both as a cutting-edge overview of existing information and as a catalyst for inspiring new studies. Computational Methods for Protein Folding is the 120th volume in the acclaimed series Advances in Chemical Physics, a compilation of scholarly works dedicated to the dissemination of contemporary advances in chemical physics, edited by Nobel Prize-winner Ilya Prigogine.

Book Biocomputing 2003   Proceedings Of The Pacific Symposium

Download or read book Biocomputing 2003 Proceedings Of The Pacific Symposium written by Russ B Altman and published by World Scientific. This book was released on 2002-12-03 with total page 671 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Pacific Symposium on Biocomputing (PSB 2003) is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. The rigorously peer-reviewed papers and presentations are collected in this archival proceedings volume.PSB 2003 brings together top researchers from the US, the Asia-Pacific region and around the world to exchange research findings and address open issues in all aspects of computational biology. PSB is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.

Book Global Minimization of Nonconvex Energy Functions  Molecular Conformation and Protein Folding

Download or read book Global Minimization of Nonconvex Energy Functions Molecular Conformation and Protein Folding written by Panos M. Pardalos and published by American Mathematical Soc.. This book was released on 1996 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work contains refereed papers presented at an interdisciplinary scientific meeting attended by a mix of leading biochemists and computer scientists held at DIMACS in March 1995. It describes the development of a variety of new methods which are being developed for attacking the important problem of molecular structure. It is intended for graduate students and researchers in numerical analysis, molecular biology, biochemistry, computer science, engineering, and operations.