Structural Classification of Proteins

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.

Originally published in 1995cite journal | author = Murzin AG, Brenner SE, Hubbard T, Chothia C | title = SCOP: a structural classification of proteins database for the investigation of sequences and structures | journal = J. Mol. Biol. | volume = 247 | issue = 4 | pages = 536–40 | year = 1995 | pmid = 7723011 | doi = 10.1006/jmbi.1995.0159 ] it is usually updated at least once yearly by Alexei G. Murzin and his colleagues,cite journal | author = Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG | title = SCOP database in 2002: refinements accommodate structural genomics | journal = Nucleic Acids Res. | volume = 30 | issue = 1 | pages = 264–7 | year = 2002 | pmid = 11752311 | doi = 10.1093/nar/30.1.264 ] cite journal | author = Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG | title = SCOP database in 2004: refinements integrate structure and sequence family data | journal = Nucleic Acids Res. | volume = 32 | issue = Database issue | pages = D226–9 | year = 2004 | pmid = 14681400 | doi = 10.1093/nar/gkh039 ] upon whose expertise the classification rests.

Hierarchical structure

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.

tructural classes

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

Wikilinks to SCOP

To cite a particular SCOP page in Wikipedia, use the template of the form |xxxxxx, where xxxxxx is a SCOP accession number, for instance SCOP|46456.

ee also

*CATH
*FSSP

References

External links

* [http://scop.mrc-lmb.cam.ac.uk/scop/ Structural Classification of Proteins]
* [http://navi.services.came.sbg.ac.at/bin/qCOPS.html qSCOP — SCOP Quantified by Structural Relationships]
* [http://supfam.org/SUPERFAMILY/ SUPERFAMILY] Library of HMMs representing SCOP superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms


Wikimedia Foundation. 2010.

Look at other dictionaries:

  • Structural alignment — is a form of sequence alignment based on comparison of shape. These alignments attempt to establish equivalences between two or more polymer structures based on their shape and three dimensional conformation. This process is usually applied to… …   Wikipedia

  • Structural motif — In an unbranched, chain like biological molecule, such as a protein or a strand of RNA, a structural motif is a three dimensional structural element or fold within the chain, which appears also in a variety of other molecules. In the context of… …   Wikipedia

  • Orientations of Proteins in Membranes database — Orientations of Proteins in Membranes Content Description The database provides spatial arrangement of proteins in the lipid bilayer Data types captured Protein structures from the PDB Organism(s) All …   Wikipedia

  • List of proteins — A list of proteins (and protein complexes). This list aims to organize information on the protein universe. All proteins can be found in the human proteome unless marked with a % .If a protein has an EC number, it should be on List of enzymes and …   Wikipedia

  • Virus classification — is the process of naming viruses and placing them into a taxonomic system. Similar to the classification systems used for cellular organisms, virus classification is the subject of ongoing debate and proposals. This is mainly due to the pseudo… …   Wikipedia

  • Protein structure — Proteins are an important class of biological macromolecules present in all biological organisms, made up of such elements as carbon, hydrogen, nitrogen, phosphorus, oxygen, and sulfur. All proteins are polymers of amino acids. The polymers, also …   Wikipedia

  • SCOP — Structural Classification Of Proteins (Medical » Human Genome) * Standing Conference Of Principals (Community » Educational) * Scoot.Com PLC (Business » NASDAQ Symbols) * Scopolamine Hydrochloride (Medical » Physiology) …   Abbreviations dictionary

  • Protein domain — Pyruvate kinase, a protein from three domains (PDB 1pkn) A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three… …   Wikipedia

  • X-ray crystallography — can locate every atom in a zeolite, an aluminosilicate with many important applications, such as water purification. X ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X rays strikes a… …   Wikipedia

  • Lysozym — C (Gallus gallus) Struktur von Lysozym nach PDB  …   Deutsch Wikipedia

Share the article and excerpts

Direct link
Do a right-click on the link above
and select “Copy Link”