Structural Classification of Proteins

From Wikipedia, the free encyclopedia

The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of 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.

This classification is more significantly based on the human expertise than semi-automatic CATH, its chief rival. It is usually accepted that SCOP provides a better justified classification. Most difficult question is decision-making if two structurally similar proteins are "evolutionary related" and therefore should be assigned to the same superfamily. This requires human expertise. Another database, FSSP, is purely automatically generated (including regular automatic updates) but offers no classification, allowing the user to draw their own conclusion as to the significance of structural relationships based on the pairwise comparisons of individual protein structures.

SCOP utilizes four levels of hierarchic structural classification:

class - general "structural architecture" of the domain
fold - similar arrangement of regular secondary structures but without evidence of evolutionary relatedness
superfamily - sufficient structural similarity to infer a divergent evolutionary relationship but no detectable sequence homology
family - some sequence similarity can be detected.

SCOP includes the following structural classes:

α-helical domains
β-sheet domains
domains from "beta-alpha-beta" structural units that form mainly parallel β-sheets
domains from independently formed α-helices and mainly antiparallel β-sheets
multidomain proteins
membrane and cell surface proteins and peptides (not including those involved in the immune system)
"small" proteins
coiled-coil proteins
low-resolution protein structures
peptides and fragments
designed proteins of non-natural sequence

[edit] See also

CATH
FSSP

[edit] References

Murzin AG, Brenner SE, Hubbard TJP, Chothia C (1995). "SCOP: a structural classification of proteins database for the investigation of sequences and structures". J. Mol. Biol. 247: 536-540.
Lo Conte L, Brenner SE, Hubbard TJP, Chothia C, Murzin AG (2002). "SCOP database in 2002: refinements accommodate structural genomics". Nucl. Acid Res. 30 (1): 264-267.
Andreeva A., Howorth D., Brenner S.E., Hubbard T.J.P., Chothia C., Murzin A.G. (2004). "SCOP database in 2004: refinements integrate structure and sequence family data". Nucl. Acid Res. 32: D226-D229.