Protein Geometry, Classification, Topology and Symmetry: A Computational Analysis of Structure

INTRODUCTION Prologue Basic Principles of Protein Structure GEOMETRY Ellipsoids and Embedding Geometric Representations of Structure Distance Geometry Sticks to Strings Secondary Structure Geometries Simplified Architectures Sheets and Barrels Beta-Sheet Geometry Beta-Barrels CLASSIFICATION Networks and Domains Hydrogen-Bond Networks Protein Domain Definitions Protein Structure Comparison Overview of Comparison Methods Assessment of Significance Classification and Fold Spaces Protein Structure Classification Protein Fold Spaces A "Periodic Table" for Protein Structures Evolutionary' steps in fold-space TOPOLOGY Folds, Tangles and Knots Topology and Knots Random Walks in Fold-Space Protein Fold Complexity Structure Prediction and Modelling Random Folds from Distance Geometry Modelling with Distance Geometry Protein Tertiary Structure Prediction SYMMETRY Structural Symmetry Symmetry A Fourier Analysis of Symmetry Evolution and Origins Evolution of Structure and Function The Origins of Proteins The Secret of Life References Index