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Data growth and its impact on the SCOP database



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Published online 13 November 2007 Nucleic Acids Research 2008 Vol 36 Database issue D419 D425 doi 10 1093 nar gkm993 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 1 MRC 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 4 Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA and 5MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Received September 14 2007 Revised October 19 2007 Accepted October 22 2007 ABSTRACT 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



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