Computational and visualization techniques for structural bioinformatics using chimera / Forbes J. Burkowski, University of Waterloo, Ontario, Canada.

Format:

Book

Author/Creator:

Burkowski, Forbes J., author.

Series:

Chapman and Hall/CRC mathematical & computational biology series.

Chapman & Hall/CRC Mathematical and Computational Biology Series

Language:

English

Subjects (All):

Structural bioinformatics--Simulation methods.

Structural bioinformatics.

Molecular structure--Mathematical models.

Molecular structure.

Proteins--Analysis--Data processing.

Proteins.

Physical Description:

1 online resource (453 p.)

Edition:

1st ed.

Place of Publication:

Boca Raton, [Florida] ; London, [England] ; New York : CRC Press, 2015.

Language Note:

English

Summary:

"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"-- Provided by publisher.

"Goals of this book while attending a workshop or conference on Structural Bioinformatics you may overhear tidbits of conversations that are interspersed with phrases such as "phosphofructokinase regulation", "singular value decomposition", or "class instantiation". The usage of such terminology, arising from biochemistry, mathematics, and computer science respectively would not be surprising in this setting because these three areas of investigation have become the core of expertise required for the study of structural bioinformatics:"-- Provided by publisher.

Contents:

Front Cover

Dedication

Contents

Preface

Acknowledgments

Author

Chapter 1: Introduction: Macromolecules and Chimera

Chapter 2: Accessing and Displaying Molecular Data with Chimera

Chapter 3: Algorithms Dealing with Distance

Chapter 4: Algorithms Dealing with Angles

Chapter 5: Structure Overlap and Alignment

Chapter 6: Potential Energy Functions

Chapter 7: Rotamers and Side-Chain Conformation

Chapter 8: Residue Networks

Appendix A: Simple Dialogs

Appendix B: Scenographics

Appendix C: The Graph Class

Appendix D: 2D and 3D Plots

Appendix E: Dynamic Programming

Color Insert.

Notes:

Bibliographic Level Mode of Issuance: Monograph

Description based on print version record.

ISBN:

1-04-006853-7

1-4398-3662-0

9780429151439

OCLC:

905921469