Protein Bioinformatics

An Algorithmic Approach to Sequence and Structure Analysis

Author: Ingvar Eidhammer,Inge Jonassen,William R. Taylor

Publisher: John Wiley & Sons

ISBN: N.A

Category: Mathematics

Page: 355

View: 5056

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Pairwise global alignment of sequences. Pairwise local alignment and database search. Statical analysis. Multiple global alignment and phylogenetic trees. Scoring matrices. Profiles. Sequence patterns. Structures and structure descriptions. Superposition and Dynamic programming. Geometric techniques. Clustering: Combining local similarities. Significance and assessment of structure comparisons. Multiple structure comparison. Protein structure classification. Structure prediction: Threading. Basics in mathematics, probability and algorithms. Introduction to molecular biology.
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The Ten Most Wanted Solutions in Protein Bioinformatics

Author: Anna Tramontano

Publisher: CRC Press

ISBN: 1420035002

Category: Mathematics

Page: 216

View: 4111

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Utilizing high speed computational methods to extrapolate to the rest of the protein universe, the knowledge accumulated on a subset of examples, protein bioinformatics seeks to accomplish what was impossible before its invention, namely the assignment of functions or functional hypotheses for all known proteins. The Ten Most Wanted Solutions in Protein Bioinformatics considers the ten most significant problems occupying those looking to identify the biological properties and functional roles of proteins. - Problem One considers the challenge involved with detecting the existence of an evolutionary relationship between proteins. - Two and Three studies the detection of local similarities between protein sequences and analysis in order to determine functional assignment. - Four, Five, and Six look at how the knowledge of the three-dimensional structures of proteins can be experimentally determined or inferred, and then exploited to understand the role of a protein. - Seven and Eight explore how proteins interact with each other and with ligands, both physically and logically. - Nine moves us out of the realm of observation to discuss the possibility of designing completely new proteins tailored to specific tasks. - And lastly, Problem Ten considers ways to modify the functional properties of proteins. After summarizing each problem, the author looks at and evaluates the current approaches being utilized, before going on to consider some potential approaches.
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Protein Bioinformatics

From Sequence to Function

Author: M. Michael Gromiha

Publisher: Academic Press

ISBN: 0123884241

Category: Computers

Page: 339

View: 8000

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One of the most pressing tasks in biotechnology today is to unlock the function of each of the thousands of new genes identified every day. Scientists do this by analyzing and interpreting proteins, which are considered the task force of a gene. This single source reference covers all aspects of proteins, explaining fundamentals, synthesizing the latest literature, and demonstrating the most important bioinformatics tools available today for protein analysis, interpretation and prediction. Students and researchers of biotechnology, bioinformatics, proteomics, protein engineering, biophysics, computational biology, molecular modeling, and drug design will find this a ready reference for staying current and productive in this fast evolving interdisciplinary field. Explains all aspects of proteins including sequence and structure analysis, prediction of protein structures, protein folding, protein stability, and protein interactions Presents a cohesive and accessible overview of the field, using illustrations to explain key concepts and detailed exercises for students.
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Structural bioinformatics

an algorithmic approach

Author: F. J. Burkowski

Publisher: Chapman & Hall

ISBN: N.A

Category: Computers

Page: 406

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As the field of bioinformatics grows, the progression of topics in the field reflects separate concerns for sequence data and structure data. This book presents key algorithms - some developed within the artificial intelligence community - and their applications to problems in structural biology and drug discovery.
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Introduction to Bioinformatics

A Theoretical And Practical Approach

Author: Stephen A. Krawetz

Publisher: Springer Science & Business Media

ISBN: 9781588290649

Category: Computers

Page: 746

View: 1033

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A comprehensible introduction to the key biological, mathematical, statistical, and computer concepts and tools behind bioinformatics. For physical scientists, the book provides a sound biological framework for understanding the questions a life scientist would ask in the context of currently available computational tools. For life scientists, a complete discussion of the UNIX operating system offers biologists graphical-user-interface comfort in a command-line environment, plus an understanding of the installation and management of UNIX-based software tools. In the applications sections the book provides a common meeting ground for life and physical scientists. Here they will find examples of the management and analysis of DNA sequencing projects, the modeling of DNA as a statistical series of patterns, various methods of pattern discovery, protein visualization, and the use of multiple sequence alignment to infer both functional and structural biological relationships. An accompanying CD contains several full and limited trial-versions of the programs discussed in the text, as well as a complete set of illustrations from each chapter suitable for lectures and presentations.
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Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics

Author: Yi Pan,Jianxin Wang,Min Li

Publisher: John Wiley & Sons

ISBN: 1118567811

Category: Medical

Page: 536

View: 7043

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An in-depth look at the latest research, methods, and applications in the field of protein bioinformatics This book presents the latest developments in protein bioinformatics, introducing for the first time cutting-edge research results alongside novel algorithmic and AI methods for the analysis of protein data. In one complete, self-contained volume, Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics addresses key challenges facing both computer scientists and biologists, arming readers with tools and techniques for analyzing and interpreting protein data and solving a variety of biological problems. Featuring a collection of authoritative articles by leaders in the field, this work focuses on the analysis of protein sequences, structures, and interaction networks using both traditional algorithms and AI methods. It also examines, in great detail, data preparation, simulation, experiments, evaluation methods, and applications. Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics: Highlights protein analysis applications such as protein-related drug activity comparison Incorporates salient case studies illustrating how to apply the methods outlined in the book Tackles the complex relationship between proteins from a systems biology point of view Relates the topic to other emerging technologies such as data mining and visualization Includes many tables and illustrations demonstrating concepts and performance figures Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics is an essential reference for bioinformatics specialists in research and industry, and for anyone wishing to better understand the rich field of protein bioinformatics.
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Structural Bioinformatics

Author: Jenny Gu,Philip E. Bourne

Publisher: John Wiley & Sons

ISBN: 0470181052

Category: Computers

Page: 1035

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The second edition of this successful text expands on the depth and scope of the topic by bringing together many of the world's experts to provide a view of the current state of the field suitable for advanced undergraduate students, graduate students and beyond. The book begins with a description of the principles of protein, DNA and RNA structure, the methods used to collect the data, and how the data are represented, visualized and stored. With these prerequisites the comparative analysis of structure reveals classification schemes and how they are used in studies ranging from evolution to structure prediction. The physical properties of structure are explored to understand, for example, how macromolecules move and interact with each other and with ligands, offering insights into how drug discovery is undertaken and how structure can provide the details needed to understand complex molecular interactions important in fields such as immunology and systems biology. Finally, structural genomics reveals insight into the future role of structural bioinformatics where features, including function, are systematically assigned and the structural basis of complete organisms begin to emerge.
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Bioinformatics: Genomics and Proteomics

Author: Ruchi Singh

Publisher: Vikas Publishing House

ISBN: 9325978555

Category: Technology & Engineering

Page: N.A

View: 2969

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This is an innovative textbook for undergraduates as well as postgraduates offering basic knowledge of biology. Its aim is to provide state-of-the-art information about this developing science that has the potential to replace existing biological approaches to study genes and proteins. The chapters are explained in a concise yet detailed manner, including ample cross-references, references to literature and databases, tables and illustrations. The book's sound approach to this intricately complex field makes it an exceptional resource for further exploration into biochemistry, molecular biology, genomics and drug designing fields. Abundant learning features make this book the ideal teaching and learning tool. KEY FEATURES • Illustrations to bolster understanding of complex biochemical relations • Tables for quick access to precise data • Extensive end-of-chapter exercises and references • The most basic details furnished for those who are new to biology • User-friendly, Internet-based bioinformatics tools that allow researchers to extract information from databases and analyze it • Analysis of one software tool discussed in each chapter step-by-step from entering the input till interpretation of the results This is an in-depth textbook written for the biologist who wants a thorough understanding of the popular bioinformatics programs and molecular databases currently in use. It provides a broad, application-oriented overview of this technology.
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Bioinformatics Research and Development

Second International Conference, BIRD 2008, Vienna, Austria, July 7-9, 2008 Proceedings

Author: Mourad Elloumi,Josef Küng,Michal Linial,Robert Murphy,Kristan Schneider,Cristian Toma

Publisher: Springer Science & Business Media

ISBN: 3540706003

Category: Science

Page: 596

View: 7742

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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.
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A Metaheuristic Approach to Protein Structure Prediction

Algorithms and Insights from Fitness Landscape Analysis

Author: Nanda Dulal Jana,Swagatam Das,Jaya Sil

Publisher: Springer

ISBN: 3319747754

Category: Computers

Page: 220

View: 9807

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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.
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