Protein Structure Classification

Frances MG Pearl, University College London, London, UK
Christine A Orengo, University College London, London, UK
Janet M Thornton, European Bioinformatics Institute, Hinxton, Cambridge, UK

Published online: September 2007

DOI: 10.1002/9780470015902.a0003033.pub2

To understand and map the universe of protein structures, it is necessary to collate, annotate and classify these structures in a rational scheme. The different approaches that have been taken to tackle this problem include the identification of protein domains, phylogenetic and phenetic classification and hierarchical and nearest-neighbour clustering. Powerful new sequence searching methods enable structural assignments to be allocated to genomic data.

Keywords: protein structure classification; common folds; protein architecture; structural comparison; genomes

Figure 1. Schematic representation of the Class (C), Architecture (A) and Topology/fold (T) levels in the CATH database.
Figure 2. CATHerine wheel plot showing the distribution of nonhomologous structures (i.e. a single representative from each homologous superfamily (H-level) in CATH) among the different classes (C), architectures (A), and fold families (T) in the CATH database. Protein classes are shown pink (mainly ), yellow (mainly ) and green (). Within each class, the angle subtended for a given segment reflects the proportion of structures within the identified architectures (inner circle) or fold families (outer circle). The superfold families are indicated in paler colours and illustrated with a MOLSCRIPT drawing of a representative from the family.
Figure 3. Schematic showing the difference between shear (sliding) and hinge motions.
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 Further Reading
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    book Bourne PE and Weissig H (eds) (2003) Structural Bioinformatics. Hoboken, NJ: Wiley-Liss.
    book Orengo CA, Thornton JM and Jones DT (eds) (2003) Bioinformatics: Genes, Proteins & Computers. Oxford: BIOS Scientific.
    book Schulz GE and Schirmer RH (1979) Principles of Protein Structure. New York: Springer-Verlag.

Related Sub-Topics:

Protein Structure | Proteins: Structure, Function, Metabolism
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Article Title: Protein Structure Classification
 
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Pearl, Frances MG, Orengo, Christine A, and Thornton, Janet M(Sep 2007) Protein Structure Classification. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0003033.pub2]