The Classification of Protein Domains

The significant expansion in protein sequence and structure data that we are now witnessing brings with it a pressing need to bring order to the protein world. Such order enables us to gain insights into the evolution of proteins, their function and the extent to which the functional repertoire can vary across the three kingdoms of life. This has lead to the creation of a wide range of protein family classifications that aim to group proteins based upon their evolutionary relationships.In this chapter we discuss the approaches and methods that are frequently used in the classification of proteins, with a specific emphasis on the classification of protein domains. The construction of both domain sequence and domain structure databases is considered and we show how the use of domain family annotations to assign structural and functional information is enhancing our understanding of genomes.