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

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 keep...

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Autores principales: Andreeva, Antonina, Howorth, Dave, Chandonia, John-Marc, Brenner, Steven E., Hubbard, Tim J. P., Chothia, Cyrus, Murzin, Alexey G.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238974/
https://www.ncbi.nlm.nih.gov/pubmed/18000004
http://dx.doi.org/10.1093/nar/gkm993
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author Andreeva, Antonina
Howorth, Dave
Chandonia, John-Marc
Brenner, Steven E.
Hubbard, Tim J. P.
Chothia, Cyrus
Murzin, Alexey G.
author_facet Andreeva, Antonina
Howorth, Dave
Chandonia, John-Marc
Brenner, Steven E.
Hubbard, Tim J. P.
Chothia, Cyrus
Murzin, Alexey G.
author_sort Andreeva, Antonina
collection PubMed
description 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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spelling pubmed-22389742008-02-12 Data growth and its impact on the SCOP database: new developments Andreeva, Antonina Howorth, Dave Chandonia, John-Marc Brenner, Steven E. Hubbard, Tim J. P. Chothia, Cyrus Murzin, Alexey G. Nucleic Acids Res Articles 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. Oxford University Press 2008-01 2007-11-13 /pmc/articles/PMC2238974/ /pubmed/18000004 http://dx.doi.org/10.1093/nar/gkm993 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ 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.
spellingShingle Articles
Andreeva, Antonina
Howorth, Dave
Chandonia, John-Marc
Brenner, Steven E.
Hubbard, Tim J. P.
Chothia, Cyrus
Murzin, Alexey G.
Data growth and its impact on the SCOP database: new developments
title Data growth and its impact on the SCOP database: new developments
title_full Data growth and its impact on the SCOP database: new developments
title_fullStr Data growth and its impact on the SCOP database: new developments
title_full_unstemmed Data growth and its impact on the SCOP database: new developments
title_short Data growth and its impact on the SCOP database: new developments
title_sort data growth and its impact on the scop database: new developments
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238974/
https://www.ncbi.nlm.nih.gov/pubmed/18000004
http://dx.doi.org/10.1093/nar/gkm993
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