Overview
Why comparing structures?
All protein structures determined experimentally, either by X-ray crystallography or NMR spectroscopy, are deposited in a centralized resource, the Protein Data Bank (PDB). A strinking feature derived from this wealth of data is that nearly all proteins have structural similarities to other proteins. Although these similarities may arise from general principles of physics and chemistry that limit the number of protein folds, they may also result from evolutionary relationships. Approaches that identify and examine these structural relationships have relied on the classifications of proteins.
Any classification of a set of objects into clusters of similar objects requires a definition and a measure of similarity and dissimilarity. In the case of proteins, such a measure is provided by structural alignments. In this chapter, we review different methods of structural alignments, as well as how these alignments are used to measure similarity. We then review the existing classifications of protein structures.
An example of structural classification
CATH is a hierarchical classification of protein structures, with class (C) at the top of the hierarchy. Proteins inside each class are further classified by architecture (A), themselves separated into different topologies (T) or folds.