Overview

"This book emphasizes computer programs that analyze protein structural data with program output generating data files and visual feedback in the form of a molecular display. The theoretical part of the text considers both the mathematical models related to molecular structure and the computational strategies that work with these models to derive results. The practical part of the text presents UCSF Chimera as a ""workbench"" that provides a Python programming environment and the ability to see program output in the molecular display. The accompanying CD-ROM includes Python code, color figures, and session files for Chimera."

Full Product Details

Author:   Forbes J. Burkowski (University of Waterloo, Ontario, Canada)
Publisher:   Taylor & Francis Inc
Imprint:   Chapman & Hall/CRC
Volume:   56
Dimensions:   Width: 15.60cm , Height: 2.50cm , Length: 23.40cm
Weight:   0.793kg
ISBN:  

9781439836613

ISBN 10:   1439836612
Pages:   461
Publication Date:   29 July 2014
Audience:   Professional and scholarly ,  College/higher education ,  Professional & Vocational ,  Tertiary & Higher Education
Format:   Hardback
Publisher's Status:   Active
Availability:   In Print  
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Table of Contents

Introduction: Macromolecules and Chimera. Accessing and Displaying Molecular Data with Chimera. Algorithms Dealing with Distance. Algorithms Dealing with Angles. Structure Overlap and Alignment. Potential Energy Functions. Rotamers and Side‑Chain Conformation. Residue Networks. Appendices. Index.

Reviews

"""This book supports an approach to bioinformatics that balances biological problems, mathematical modeling, and computational tools. It breaks down the mathematical complications into manageable parts and augments programming skills while developing biological insight."" —L. Ridgway Scott, Louis Block Professor of Computer Science and Mathematics, Member of the Institute for Biophysical Design, Senior Fellow of the Computation Institute, University of Chicago ""This book is a useful resource for experienced and newcomer Chimera users alike. It helps extend it programmatically, allowing users to perform any number of useful types of calculations that are often required in conjunction with visualization. From distances to graphs, any way you measure it, Prof. Burkowski’s book is a must have for Chimera users."" —Rafael Najmanovich, PhD, Associate Professor, Université de Sherbrooke ""Structural bioinformatics is a young science that lies at the crossroads of several synergizing disciplines, including biophysics, structural biology, mathematical modeling, and computational methods. In this context, the book by Forbes Burkowski constitutes a true landmark, enabling the practitioner to implement and exploit computational techniques to test the mathematical models and frame novel hypothesis. This engrossing book is directed at advanced undergraduates and professionals who seek to represent and explore novel structural concepts to describe biomolecular phenomena. Very useful practical applications of the computational techniques presented in the book are likely to emerge, especially in the fields of molecular engineering and structure-based drug design. Thus, I predict that the book will become mandatory for researchers interested in rational design in the pharmaceutical industry and materials science."" —Ariel Fernandez, Ph.D., Former Hasselmann Professor of Bioengineering at Rice University and Pioneer of the Wrapping Technology in Drug Design ""Students taught with Computational and Visualization Techniques for Structural Bioinformatics Using Chimera will gain not only a thorough understanding of the important concepts of structural bioinformatics, from the basics of protein structure through advanced topics such as molecular mechanics, but also the ability to perform their own analyses using the programming techniques and libraries offered by this book and its supporting materials. The exercises are engaging and vary from problems that can be solved in a few minutes to mini-projects that might require a week of effort. All concepts are clearly described and accompanied by helpful illustrations where needed. This text does an excellent job of turning students into investigators."" —Eric Pettersen, UCSF Department of Pharmaceutical Chemistry"

This book supports an approach to bioinformatics that balances biological problems, mathematical modeling, and computational tools. It breaks down the mathematical complications into manageable parts and augments programming skills while developing biological insight. -L. Ridgway Scott, Louis Block Professor of Computer Science and Mathematics, Member of the Institute for Biophysical Design, Senior Fellow of the Computation Institute, University of Chicago This book is a useful resource for experienced and newcomer Chimera users alike. It helps extend it programmatically, allowing users to perform any number of useful types of calculations that are often required in conjunction with visualization. From distances to graphs, any way you measure it, Prof. Burkowski's book is a must have for Chimera users. -Rafael Najmanovich, PhD, Associate Professor, Universite de Sherbrooke Structural bioinformatics is a young science that lies at the crossroads of several synergizing disciplines, including biophysics, structural biology, mathematical modeling, and computational methods. In this context, the book by Forbes Burkowski constitutes a true landmark, enabling the practitioner to implement and exploit computational techniques to test the mathematical models and frame novel hypothesis. This engrossing book is directed at advanced undergraduates and professionals who seek to represent and explore novel structural concepts to describe biomolecular phenomena. Very useful practical applications of the computational techniques presented in the book are likely to emerge, especially in the fields of molecular engineering and structure-based drug design. Thus, I predict that the book will become mandatory for researchers interested in rational design in the pharmaceutical industry and materials science. -Ariel Fernandez, Ph.D., Former Hasselmann Professor of Bioengineering at Rice University and Pioneer of the Wrapping Technology in Drug Design Students taught with Computational and Visualization Techniques for Structural Bioinformatics Using Chimera will gain not only a thorough understanding of the important concepts of structural bioinformatics, from the basics of protein structure through advanced topics such as molecular mechanics, but also the ability to perform their own analyses using the programming techniques and libraries offered by this book and its supporting materials. The exercises are engaging and vary from problems that can be solved in a few minutes to mini-projects that might require a week of effort. All concepts are clearly described and accompanied by helpful illustrations where needed. This text does an excellent job of turning students into investigators. -Eric Pettersen, UCSF Department of Pharmaceutical Chemistry

Structural bioinformatics is a young science that lies at the crossroads of several synergizing disciplines, including biophysics, structural biology, mathematical modeling, and computational methods. In this context, the book by Forbes Burkowski constitutes a true landmark, enabling the practitioner to implement and exploit computational techniques to test the mathematical models and frame novel hypothesis. This engrossing book is directed at advanced undergraduates and professionals who seek to represent and explore novel structural concepts to describe biomolecular phenomena. Very useful practical applications of the computational techniques presented in the book are likely to emerge, especially in the fields of molecular engineering and structure-based drug design. Thus, I predict that the book will become mandatory for researchers interested in rational design in the pharmaceutical industry and materials science. -Ariel Fernandez, Ph.D., Former Hasselmann Professor of Bioengineering at Rice University and Pioneer of the Wrapping Technology in Drug Design

Author Information

Forbes Burkowski is a professor of computer science at the University of Waterloo in Ontario, Canada.

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