Structural Classification of Proteins
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The Structural Classification of Proteins (SCOP) database is a largely manual classification of proteins based on similarities which can be observed in their amino acid sequences and three-dimensional structures.
Originally published in 1995 it is usually updated at least once yearly by Alexei G. Murzin and his colleagues, upon whose expertise the classification rests.
Although computational tools are used to assist the classification process it is the predominantly manual nature of the classification which distinguishes it from CATH, its chief rival. The FSSP database, which should also be mentioned in this context, offers another means of exploring protein structure space. FSSP is purely automatic (including regular automatic updates) but offers no classification, allowing the user to draw their own conclusion as to the significance of structural relationships.
SCOP utilises a hierarchical scheme to organise the classification, allowing a four character code to be assigned to any protein domain.
The four classification levels are:
- class - a very broad description of the structural content of the protein
- fold - indicative of a broad structural similarity but with no evidence of a homologous relationship
- superfamily - sufficient structural similarity to infer a divergent evolutionary relationship but no detectable sequence similarity
- family - significant sequence similarity which can be detected either directly or through a transitive search.
- domains - Autonomously-folding units of compact structure (some times this is listed as a fifth category).
SCOP defines the following classes: proteins with only α-helices, proteins with only β-sheets, proteins with both α-helices and mainly parallel β-sheets, proteins with both α-helices and mainly antiparallel β-sheets, multidomain proteins, membrane and cell surface proteins and peptides (not immune system proteins) and small proteins.