Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics

Chapter 13

Fundamentals of Protein Structure Alignment

MARK BRANDT, ALLEN HOLDER, and YOSI SHIBBERU

13.1 Introduction

The central dogma of molecular biology asserts a one-way transfer of information from a cell's genetic code to the expression of proteins. Proteins are the functional workhorses of a cell, and studying these molecules is at the foundation of much of computational biology. Our goal here is to present a succinct introduction to the biological, mathematical, and computational aspects of making pairwise comparisons between protein structures. The presentation is intended to be useful for those who are entering this research area. The chapter begins with a brief introduction to the biology of protein comparison, which is followed by a brief taxonomy of the different mathematical frameworks for protein structure alignment. We conclude with a couple of more recent pairwise comparison techniques that are at the forefront of efficiency and accuracy. Such methods are becoming important as structural databases grow.

13.2 Biological Motivation of Protein Structure Alignment

Proteins are crucially important molecules that are responsible for a large variety of biological functions required for life to exist. The DNA sequence of the genome provides a one-dimensional descriptive code; proteins are self-organizing systems that allow expansion of this one-dimensional code into complex three-dimensional structures possessing a great diversity of functions. Understanding the types ...