Computational and Visualization Techniques for Structural Bioinformatics Using Chimera: 1st Edition (e-Book) book cover

Computational and Visualization Techniques for Structural Bioinformatics Using Chimera

1st Edition

By Forbes J. Burkowski

Chapman and Hall/CRC

461 pages | 40 Color Illus. | 189 B/W Illus.

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Description

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.

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

Table of Contents

Introduction: Macromolecules and Chimera

MOTIVATION

WHY CHIMERA?

GETTING STARTED WITH CHIMERA

OVERVIEW OF PROTEIN STRUCTURE

Accessing and Displaying Molecular Data with Chimera

MOTIVATION

PYTHON SKILLS

PYTHON SCRIPTING

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

HILITER CLASS

HBONDDICTS CLASS

Algorithms Dealing with Distance

MOTIVATION

CALCULATING INTERATOMIC DISTANCES

APPLICATIONS

RAPID DETERMINATION OF ATOM MEMBERSHIP IN SHELLS

CONTACT MAPS FOR PROTEINS

INERTIAL AXES

DEHYDRONS

Algorithms Dealing with Angles

MOTIVATION

BOND ANGLE

DIHEDRAL ANGLES

RAMACHANDRAN PLOTS

LEAST SQUARES PLANE

Structure Overlap and Alignment

MOTIVATION

INTRODUCTION

TECHNIQUES FOR STRUCTURAL COMPARISON

SCORING SIMILARITIES AND OPTIMIZING SCORES

SUPERPOSITION ALGORITHMS

A SIMPLE SCRIPT TO DO STRUCTURAL SUPERIMPOSITION

PROTEIN SEQUENCE ALIGNMENT

VARIATIONS IN THE GLOBAL ALIGNMENT ALGORITHM

PERCENT IDENTITY COMPARISON

LOCAL ALIGNMENT

A SCRIPT TO DO SEQUENCE ALIGNMENT AND THEN STRUCTURAL OVERLAP

DEALING WITH WEAKER SEQUENCE SIMILARITY

Potential Energy Functions

MOTIVATION

SOME SIMPLE SCRIPTS TO DO ENERGY CALCULATIONS

Rotamers and Side‑Chain Conformation

MOTIVATION

SIDE-CHAIN PACKING: COMPUTATIONAL ISSUES

ROTAMERICITY

ACCESSING ROTAMERS USING A PYTHON SCRIPT

ROTAMERS AND DIHEDRAL ANGLES

A SINGLE SIDE CHAIN AND ENERGY CONSIDERATIONS

SIDE-CHAIN PACKING AND DEAD-END ELIMINATION

Residue Networks

MOTIVATION

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

Index

Exercises and References appear at the end of each chapter.

About the Author

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

About the Series

Chapman & Hall/CRC Mathematical and Computational Biology

Learn more…

Subject Categories

BISAC Subject Codes/Headings:
SCI008000
SCIENCE / Life Sciences / Biology / General
SCI010000
SCIENCE / Biotechnology
SCI055000
SCIENCE / Physics