ABSTRACT

From a geometric perspective, this book 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 the 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.

chapter Chapter 1|15 pages

Introduction

part 1|114 pages

Geometry

chapter Chapter 2|30 pages

Ellipsoids and embedding

chapter Chapter 3|44 pages

Sticks to strings

chapter Chapter 4|38 pages

Sheets and barrels

part 2|78 pages

Classification

chapter Chapter 5|26 pages

Networks and domains

chapter Chapter 6|21 pages

Protein structure comparison

chapter Chapter 7|29 pages

Classification and fold spaces

part 3|60 pages

Topology

chapter Chapter 8|38 pages

Folds, tangles and knots

chapter Chapter 9|20 pages

Structure prediction and modelling

part 4|39 pages

Symmetry

chapter Chapter 10|22 pages

Structural symmetry

chapter Chapter 11|15 pages

Evolution and origins