Computational and Visualization Techniques for Structural Bioinformatics Using Chimera

Computational and Visualization Techniques for Structural Bioinformatics Using Chimera

by Forbes J. Burkowski

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Overview

Computational and Visualization Techniques for Structural Bioinformatics Using Chimera by Forbes J. Burkowski

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.

Product Details

ISBN-13: 9781439836613
Publisher: Taylor & Francis
Publication date: 08/07/2014
Series: Chapman & Hall/CRC Mathematical and Computational Biology Series , #56
Pages: 461
Product dimensions: 6.00(w) x 9.30(h) x 1.00(d)

About the Author

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

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.

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