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.
Print Versions of this book also include access to the ebook version.
Table of Contents
Introduction: Macromolecules and Chimera
GETTING STARTED WITH CHIMERA
OVERVIEW OF PROTEIN STRUCTURE
Accessing and Displaying Molecular Data with Chimera
CHIMERA OBJECT HIERARCHY
ATTRIBUTES FOR MOLECULE OBJECTS
ATTRIBUTES FOR SEQUENCE OBJECTS
ATTRIBUTES FOR RESIDUE OBJECTS
ATTRIBUTES FOR ATOM OBJECTS
ATTRIBUTES FOR BOND OBJECTS
WORKING WITH A BATCH OF FILES
Algorithms Dealing with Distance
CALCULATING INTERATOMIC DISTANCES
RAPID DETERMINATION OF ATOM MEMBERSHIP IN SHELLS
CONTACT MAPS FOR PROTEINS
Algorithms Dealing with Angles
LEAST SQUARES PLANE
Structure Overlap and Alignment
TECHNIQUES FOR STRUCTURAL COMPARISON
SCORING SIMILARITIES AND OPTIMIZING SCORES
A SIMPLE SCRIPT TO DO STRUCTURAL SUPERIMPOSITION
PROTEIN SEQUENCE ALIGNMENT
VARIATIONS IN THE GLOBAL ALIGNMENT ALGORITHM
PERCENT IDENTITY COMPARISON
A SCRIPT TO DO SEQUENCE ALIGNMENT AND THEN STRUCTURAL OVERLAP
DEALING WITH WEAKER SEQUENCE SIMILARITY
Potential Energy Functions
SOME SIMPLE SCRIPTS TO DO ENERGY CALCULATIONS
Rotamers and Side‑Chain Conformation
SIDE-CHAIN PACKING: COMPUTATIONAL ISSUES
ACCESSING ROTAMERS USING A PYTHON SCRIPT
ROTAMERS AND DIHEDRAL ANGLES
A SINGLE SIDE CHAIN AND ENERGY CONSIDERATIONS
SIDE-CHAIN PACKING AND DEAD-END ELIMINATION
THREE-DIMENSIONAL (3D) VISUALIZATION OF RESIDUE NETWORKS
ALLOSTERY AND CONTACT REARRANGEMENT NETWORKS
Appendix A: Simple Dialogs
Appendix B: Scenographics
Appendix C: The Graph Class
Appendix D: 2D and 3D Plots
Appendix E: Dynamic Programming
Exercises and References appear at the end of each chapter.
Forbes Burkowski is a professor of computer science at the University of Waterloo in Ontario, Canada.
"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