Lecture Notes On Computational Structural Biology
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Lecture Notes On Computational Structural Biology
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Author : Zhijun Wu
language : en
Publisher: World Scientific
Release Date : 2008
Lecture Notes On Computational Structural Biology written by Zhijun Wu and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with Science categories.
1. Introduction. 1.1. Protein structure. 1.2. Structure determination. 1.3. Dynamics simulation. 1.4. The myth of protein folding -- 2. X-ray crystallography computing. 2.1. The phase problem. 2.2. Least squares solutions. 2.3. Entropy maximization. 2.4. Indirect methods -- 3. NMR structure determination. 3.1. Nuclear magnetic resonance. 3.2. Distance geometry. 3.3. Distance-based modeling. 3.4. Structural analysis -- 4. Potential energy minimization. 4.1. Potential energy function. 4.2. Local optimization. 4.3. Global optimization. 4.4. Energy transformation -- 5. Molecular dynamics simulation. 5.1. Equations of motion. 5.2. Initial-value problem. 5.3. Boundary-value problem. 5.4. Normal mode analysis -- 6. Knowledge-based protein modeling. 6.1. Sequence/structural alignment. 6.2. Fold recognition/inverse folding. 6.3. Knowledge-based structural refinement. 6.4. Structural computing and beyond
Computational Structural Biology
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Author : Manuel Claude Peitsch
language : en
Publisher: World Scientific
Release Date : 2008
Computational Structural Biology written by Manuel Claude Peitsch and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with Science categories.
This work covers the impact of computational structural biology on protein structure prediction methods, macromolecular function and protein design, and key methods in drug discovery. It also addresses the computational challenges of experimental approaches in structural biology.
Algorithms In Structural Molecular Biology
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Author : Bruce R. Donald
language : en
Publisher: MIT Press
Release Date : 2023-08-15
Algorithms In Structural Molecular Biology written by Bruce R. Donald and has been published by MIT Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-08-15 with Science categories.
An overview of algorithms important to computational structural biology that addresses such topics as NMR and design and analysis of proteins.Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules. Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility. The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.
Introduction To Computational Materials Science
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Author : Richard LeSar
language : en
Publisher: Cambridge University Press
Release Date : 2013-03-28
Introduction To Computational Materials Science written by Richard LeSar and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-03-28 with Science categories.
Emphasising essential methods and universal principles, this textbook provides everything students need to understand the basics of simulating materials behavior. All the key topics are covered from electronic structure methods to microstructural evolution, appendices provide crucial background material, and a wealth of practical resources are available online to complete the teaching package. Modeling is examined at a broad range of scales, from the atomic to the mesoscale, providing students with a solid foundation for future study and research. Detailed, accessible explanations of the fundamental equations underpinning materials modelling are presented, including a full chapter summarising essential mathematical background. Extensive appendices, including essential background on classical and quantum mechanics, electrostatics, statistical thermodynamics and linear elasticity, provide the background necessary to fully engage with the fundamentals of computational modelling. Exercises, worked examples, computer codes and discussions of practical implementations methods are all provided online giving students the hands-on experience they need.
Mobility In Process Calculi And Natural Computing
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Author : Bogdan Aman
language : en
Publisher: Springer Science & Business Media
Release Date : 2011-11-03
Mobility In Process Calculi And Natural Computing written by Bogdan Aman and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-11-03 with Computers categories.
The design of formal calculi in which fundamental concepts underlying interactive systems can be described and studied has been a central theme of theoretical computer science in recent decades, while membrane computing, a rule-based formalism inspired by biological cells, is a more recent field that belongs to the general area of natural computing. This is the first book to establish a link between these two research directions while treating mobility as the central topic. In the first chapter the authors offer a formal description of mobility in process calculi, noting the entities that move: links (π-calculus), ambients (ambient calculi) and branes (brane calculi). In the second chapter they study mobility in the framework of natural computing. The authors define several systems of mobile membranes in which the movement inside a spatial structure is provided by rules inspired by endocytosis and exocytosis. They study their computational power in comparison with the classical notion of Turing computability and their efficiency in algorithmically solving hard problems in polynomial time. The final chapter deals with encodings, establishing links between process calculi and membrane computing so that researchers can share techniques between these fields. The book is suitable for computer scientists working in concurrency and in biologically inspired formalisms, and also for mathematically inclined scientists interested in formalizing moving agents and biological phenomena. The text is supported with examples and exercises, so it can also be used for courses on these topics.
Combinatorial Pattern Matching Algorithms In Computational Biology Using Perl And R
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Author : Gabriel Valiente
language : en
Publisher: CRC Press
Release Date : 2009-04-08
Combinatorial Pattern Matching Algorithms In Computational Biology Using Perl And R written by Gabriel Valiente and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-04-08 with Computers categories.
Emphasizing the search for patterns within and between biological sequences, trees, and graphs, Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R shows how combinatorial pattern matching algorithms can solve computational biology problems that arise in the analysis of genomic, transcriptomic, proteomic, metabolomic
Systemic Approaches In Bioinformatics And Computational Systems Biology Recent Advances
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Author : Lecca, Paola
language : en
Publisher: IGI Global
Release Date : 2011-12-31
Systemic Approaches In Bioinformatics And Computational Systems Biology Recent Advances written by Lecca, Paola and has been published by IGI Global this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-12-31 with Medical categories.
The convergence of biology and computer science was initially motivated by the need to organize and process a growing number of biological observations resulting from rapid advances in experimental techniques. Today, however, close collaboration between biologists, biochemists, medical researchers, and computer scientists has also generated remarkable benefits for the field of computer science. Systemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances presents new techniques that have resulted from the application of computer science methods to the organization and interpretation of biological data. The book covers three subject areas: bioinformatics, computational biology, and computational systems biology. It focuses on recent, systemic approaches in computer science and mathematics that have been used to model, simulate, and more generally, experiment with biological phenomena at any scale.
Math And Bio 2010
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Author : Lynn Arthur Steen
language : en
Publisher: MAA
Release Date : 2005
Math And Bio 2010 written by Lynn Arthur Steen and has been published by MAA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005 with Mathematics categories.
"Math and bio 2010 grew out of 'Meeting the Challenges: Education across the Biological, Mathematical and Computer Sciences,' a joint project of the Mathematical Association of America (MAA), the National Science Foundation Division of Undergraduate Education (NSF DUE), the National Institute of General Medical Sciences (NIGMS), the American Association for the Advancement of Science (AAAS), and the American Society for Microbiology (ASM)."--Foreword, p. vi
Multi Agent Based Simulations Applied To Biological And Environmental Systems
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Author : Adamatti, Diana Francisca
language : en
Publisher: IGI Global
Release Date : 2016-12-12
Multi Agent Based Simulations Applied To Biological And Environmental Systems written by Adamatti, Diana Francisca and has been published by IGI Global this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-12-12 with Computers categories.
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.
Granular Computing In Decision Approximation
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Author : Lech Polkowski
language : en
Publisher: Springer
Release Date : 2015-04-06
Granular Computing In Decision Approximation written by Lech Polkowski and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-04-06 with Technology & Engineering categories.
This book presents a study in knowledge discovery in data with knowledge understood as a set of relations among objects and their properties. Relations in this case are implicative decision rules and the paradigm in which they are induced is that of computing with granules defined by rough inclusions, the latter introduced and studied within rough mereology, the fuzzified version of mereology. In this book basic classes of rough inclusions are defined and based on them methods for inducing granular structures from data are highlighted. The resulting granular structures are subjected to classifying algorithms, notably k—nearest neighbors and bayesian classifiers. Experimental results are given in detail both in tabular and visualized form for fourteen data sets from UCI data repository. A striking feature of granular classifiers obtained by this approach is that preserving the accuracy of them on original data, they reduce substantially the size of the granulated data set as well as the set of granular decision rules. This feature makes the presented approach attractive in cases where a small number of rules providing a high classification accuracy is desirable. As basic algorithms used throughout the text are explained and illustrated with hand examples, the book may also serve as a textbook.