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SCOP

http://scop.mrc-lmb.cam.ac.uk/scop

Lo Conte, L.1, Brenner, S.E.2, Hubbard, T.J.P.3, Chothia, C.1, Murzin, A.G.4

1MRC Laboratory of Molecular Biology, Structural Studies Division, Hills Road, Cambridge CB2 2QH, UK
2Berkeley Structural Genomics Center, Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA, and Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
3Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
4MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK

Contact   loredana@mrc-lmb.cam.ac.uk


Database Description

The SCOP: Structural Classification of Proteins database [1,2] is a comprehensive ordering of all proteins of known structures, according to their structural and evolutionary relationships. A unique aspect of SCOP is that it embeds a theory of evolution as defined by a human expert rather than the necessarily more limited set of rules implemented by a series of algorithms and automatic tools. The first SCOP release in 1994 included 3,179 domains clustered into 498 families, 366 superfamilies, and 279 different folds. The first seven classes in the current release (1.59) comprise 39,893 domains, grouped into 686 different folds, 1,073 superfamilies, and 1,827 families. These domains correspond to 15,979 entries in the Protein Data Bank (PDB) [3] and 30 references from the literature for which no experimental coordinates are available. The ten-fold increase in the number of domains since 1994 roughly means twice as many folds, 2.5 times as many superfamilies, and three times as many families. The growth in content of the SCOP database closely tracks the corresponding growth in the number of deposited structures. In the last three years SCOP has been released every 4-6 months, and included the classification of all proteins whose coordinates were available in the PDB at the time of the release. A set of new features was introduced in SCOP 1.55 [2] with the aim of standardizing access to it and providing a solid basis to cope with the increasing number of protein structures expected to be determined in the years to come in the context of various structural genomics projects. SCOP identifiers are stable. Releases starting with 1.48,are now available online at MRC site. A full history, comprising a list of new folds, superfamilies, and families, and a method to track changes to the structure of the classification itself has been introduced in SCOP 1.59. Official sequence and coordinate data for SCOP domains are available at the associated ASTRAL web site: http://astral.stanford.edu/ [4].

Recent Developments

Previous SCOP releases, starting with 1.48, are now available online at http://scop.mrc-lmb.cam.ac.uk/scop/index_prevrel.html. The new set of identifiers introduced in SCOP 1.55 is stable. An identifier always refers to the same entry. If the entry was modified, the old identifier becomes obsolete and the user is redirected to the corresponding new entry in the current release. In this way, it is possible for a user to track changes to the classification itself. Starting with release 1.59, a list of new folds, superfamilies, and families, as well entries which become obsolete is available online from the SCOP main page or can be retrieved via the SCOP search engine. Keywords of particular interest, like 'structural genomics protein', have been added to SCOP entries and allow to retrieve the corresponding set using the search engine.

REFERENCES

1) Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995)
SCOP: a structural classification of proteins database for the
investigation of sequences and structures.
J. Mol. Biol. 247, 536-540.
2) Lo Conte L., Brenner, S. E. , Hubbard T. J. P., Chothia C., and Murzin A.G. (2002)
SCOP database in 2002: refinements accommodate structural genomics.
Nucl. Acids. Res. 30, 264-267.
3) Berman, H.M. ,Westbrook, J., Feng, Z.,Gilliland, G.,Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne:, P.E. (2000)
The Protein Data Bank.
Nucleic Acids Res. 28, 235-242.
4) Brenner S.E., Koehl P., Levitt M. (2002)
ASTRAL compendium enhancements.
Nucl. Acids. Res. 30, 260-263

Category   Structure

Go to the abstract in the NAR 2002 Database Issue.

 

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