Structural Classification of Proteins
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.
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 and functional similarity to infer a divergent evolutionary relationship but not necessarily detectable sequence homology
- family - some sequence similarity can be detected.
Comparison to other classification systems
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. Human expertise is needed to decide whether certain proteins are evolutionary related and therefore should be assigned to the same superfamily, or their similarity is a result of structural constraints and therefore they belong to the same fold. 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 includes the following structural classes:
- α-helical domains
- β-sheet domains
- α/β domains which consist of from "beta-alpha-beta" structural units or "motifs" that form mainly parallel β-sheets
- α+β domains formed by independent α-helices and mainly antiparallel β-sheets
- multi-domain 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
- Murzin AG, Brenner SE, Hubbard T, Chothia C (1995). "SCOP: a structural classification of proteins database for the investigation of sequences and structures". J. Mol. Biol. 247 (4): 536–40. doi:10.1006/jmbi.1995.0159. PMID 7723011.
- Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG (2002). "SCOP database in 2002: refinements accommodate structural genomics". Nucleic Acids Res. 30 (1): 264–7. doi:10.1093/nar/30.1.264. PMID 11752311.
- Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG (2004). "SCOP database in 2004: refinements integrate structure and sequence family data". Nucleic Acids Res. 32 (Database issue): D226–9. doi:10.1093/nar/gkh039. PMID 14681400.
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