Fundamentals of Protein Structure Alignment

The chapter presents 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 such as contact map overlap (CMO) problem and the largest common point set (LCP) problem for protein structure alignment. The chapter concludes 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.