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Nucleic Acids Research Advance Access published online on November 13, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm993
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

Data growth and its impact on the SCOP database: new developments

Antonina Andreeva1,*, Dave Howorth1, John-Marc Chandonia2,3, Steven E. Brenner2, Tim J. P. Hubbard4, Cyrus Chothia5 and Alexey G. Murzin1

1MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK, 2Department of Plant and Microbial Biology, 461A Koshland Hall 3102, University of California, Berkeley, CA 94720-3102, 3Physical Biosciences Division, Berkeley National Laboratory, 1 Cyclotron Rd, Mail Stop Donner, Berkeley, CA 94720, USA, 4Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA and 5MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK

*To whom correspondence should be addressed. Tel: +44 1223 402132; Fax: +44 1223 402140; Email: tony{at}mrc-lmb.cam.ac.uk Correspondence may also be addressed to Alexey G. Murzin. Tel: +44 402132; Fax: +44 402140; Email: agm{at}mrc-lmb.cam.ac.uk

Received September 14, 2007. Revised October 19, 2007. Accepted October 22, 2007.

The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. The SCOP hierarchy comprises the following levels: Species, Protein, Family, Superfamily, Fold and Class. While keeping the original classification scheme intact, we have changed the production of SCOP in order to cope with a rapid growth of new structural data and to facilitate the discovery of new protein relationships. We describe ongoing developments and new features implemented in SCOP. A new update protocol supports batch classification of new protein structures by their detected relationships at Family and Superfamily levels in contrast to our previous sequential handling of new structural data by release date. We introduce pre-SCOP, a preview of the SCOP developmental version that enables earlier access to the information on new relationships. We also discuss the impact of worldwide Structural Genomics initiatives, which are producing new protein structures at an increasing rate, on the rates of discovery and growth of protein families and superfamilies. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.


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