Computational and Visualization Techniques for Structural Bioinformatics Using Chimera

A Step-by-Step Guide to Describing Biomolecular Structure

Computational and Visualization Techniques for Structural Bioinformatics Using Chimera shows how to perform computations with Python scripts in the Chimera environment. It focuses on the three core areas needed to study structural bioinformatics: biochemistry, mathematics, and computation.

Understand Important Concepts of Structural Bioinformatics

The book covers topics that deal primarily with protein structure and includes many exercises that are grounded in biological problems at the molecular level. The text encourages mathematical analysis by providing a firm foundation for computations. It analyzes numerous Python scripts for the Chimera environment, with the scripts and other material available on a supplementary website.

Build Python Scripts to Extend the Capabilities of Chimera

Through more than 60 exercises that involve the development of Python scripts, the book gives you concrete guidance on using the scripting capabilities of Chimera. You’ll gain experience in solving real problems as well as understand the various applications of linear algebra. You can also use the scripts as starting points for the development of similar applications and use classes from the StructBio toolkit for computations, such as structure overlap, data plotting, scenographics, and display of residue networks.

Table of Contents

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