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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 recent pairwise comparison techniques that are at the forefront of efficiency and accuracy. Such methods are becoming important as structural databases grow.


MSTR 12-01