Nucleic Acids Research

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Nucleic Acids Research, 2000, Vol. 28, No. 1 257-259
© 2000 Oxford University Press

SCOP: a Structural Classification of Proteins database

Loredana Lo Conte^*, Bart Ailey, Tim J. P. Hubbard², Steven E. Brenner³, Alexey G. Murzin¹ and Cyrus Chothia

MRC Laboratory of Molecular Biology and ¹Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK, ²Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and ³Department of Structural Biology, Stanford University, Stanford, CA 94305-5400, USA

The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of known protein structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and distant evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database so far. The sequences of proteins in SCOP provide the basis of the ASTRAL sequence libraries that can be used as a source of data to calibrate sequence search algorithms and for the generation of statistics on, or selections of, protein structures. Links can be made from SCOP to PDB-ISL: a library containing sequences homologous to proteins of known structure. Sequences of proteins of unknown structure can be matched to distantly related proteins of known structure by using pairwise sequence comparison methods to find homologues in PDB-ISL. The database and its associated files are freely accessible from a number of WWW sites mirrored from URL http://scop.mrc-lmb. cam.ac.uk/scop/

^* To whom correspondence should be addressed. Tel: +44 1223 402010; Fax: +44 1223 213556; Email: loredana@mrc-lmb.cam.ac.uk

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