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

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Auteur(s) : Forbes J Burkowski

Editeur : Crc Press

Langue : Anglais

Parution : 01/08/2014

Format : Moyen, de 350g à 1kg

Nombre de pages : 461

Expédition : 771

Dimensions : 23.6 x 15.7 x 2.5

ISBN : 1439836612

Résumé :

This book shows how to perform computations with Python scripts in the Chimera environment. It covers topics that deal primarily with protein structure and encourages mathematical analysis by providing a firm foundation for computations. Through more than 60 exercises that involve the development of Python scripts, the book gives readers concrete guidance on using the scripting capabilities of Chimera. Python scripts and other material are available on a supplementary website.

Biographie:

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

Sommaire:
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.