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More About This Textbook
Overview
Using a geometric perspective, Protein Geometry, Classification, Topology, and Symmetry reviews and analyzes the structural principals of proteins with the goal of revealing the underlying regularities in their construction. It also reviews computer methods for structure analysis and the automatic comparison and classification of these structures with an analysis of the statistical significance of comparing different shapes. Following an analysis of the current state of protein classification, the authors explore more abstract geometric and topological representations, including the occurrence of knotted topologies. The book concludes with a consideration of the origin of higher-level symmetries in protein structure.
The authors focus on simple geometric methods that are deterministic rather than probabilistic and on the more abstract simplifications of protein structure that allow a better understanding of the overall fold of the structure. Most of the methods described in this book have corresponding computer programs. These can be found (as C source code) at the ftp site of the Division of Mathematical Biology at the National Institute for Medical Research. This collection of ideas contains pedagogical material that make it ideal for post-graduate courses as well as new ideas and results essential for researchers investigating protein structures.
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Table of Contents
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