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Titolo:
Protein structural domains: analysis of the 3Dee domains database
Autore:
Dengler, U; Siddiqui, AS; Barton, GJ;
Indirizzi:
European Bioinformat Inst, EMBL, Cambridge CB10 1SD, England European Bioinformat Inst Cambridge England CB10 1SD e CB10 1SD, England Univ Oxford, Mol Biophys Lab, Oxford OX1 3QU, England Univ Oxford OxfordEngland OX1 3QU Biophys Lab, Oxford OX1 3QU, England
Titolo Testata:
PROTEINS-STRUCTURE FUNCTION AND GENETICS
fascicolo: 3, volume: 42, anno: 2001,
pagine: 332 - 344
SICI:
0887-3585(20010215)42:3<332:PSDAOT>2.0.ZU;2-I
Fonte:
ISI
Lingua:
ENG
Soggetto:
X-RAY STRUCTURE; CRYSTAL-STRUCTURE; ANGSTROM RESOLUTION; 3-DIMENSIONAL STRUCTURE; SECONDARY STRUCTURES; STRUCTURE ALIGNMENT; GLOBULAR-PROTEINS; FOLD RECOGNITION; IDENTIFICATION; CLASSIFICATION;
Keywords:
protein domain; classification; database; protein structure; protein fold;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
67
Recensione:
Indirizzi per estratti:
Indirizzo: Barton, GJ European Bioinformat Inst, EMBL, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England European Bioinformat Inst Wellcome Trust GenomeCampus Cambridge England CB10 1SD
Citazione:
U. Dengler et al., "Protein structural domains: analysis of the 3Dee domains database", PROTEINS, 42(3), 2001, pp. 332-344

Abstract

The 3Dee database of domain definitions was developed as a comprehensive collection of domain definitions for all three-dimensional structures in theProtein Data Bank (PDB), The database includes definitions for complex, multiple-segment and multiple-chain domains as well as simple sequential domains, organized in a structural hierarchy. Two different snapshots of the 3Dee database were analyzed at September 1996 and November 1999, For the November 1999 release, 7,995 PDB entries contained 13,767 protein chains and gave rise to 18,896 domains. The domain sequences clustered into 1,715 domainsequence families, which were further clustered into a conservative 1,199 domain structure families (families with similar folds). The proportion of different domain structure families per domain sequence family increases from 84% for domains 1-100 residues long to 100% for domains greater than 600residues. This is in keeping with the idea that longer chains will have more alternative folds available to them, Of the representative domains from the domain sequence families, 49% are in the range of 51-150 residues, whereas 64% of the representative chains over 200 residues have more than 1 domain. Of the representative chains, 8.5% are part of multichain domains. Thelargest multichain domain in the database has 14 chains and 1,400 residues, whereas the largest single-chain domain has 907 residues. The largest number of domains found in a protein is 13, The analysis shows that over the history of the PDB, new domain folds have been discovered at a slower rate than by random selection of all known folds. Between 1992 and 1997, a constant 1 in 11 new domains deposited in the PDB has shown no sequence similarity to a previously known domain sequence family, and only 1 in 15 new domainstructures has had a fold that has not been seen previously. A comparison of the September 1996 release of 3Dee to the Structural Classification of Proteins (SCOP) showed that the domain definitions agreed for 80% of the representative protein chains. However, 3Dee provided explicit domain boundaries for more proteins, 3Dee is accessible on the World Wide Web at http://barton.ebi.ac.uk/servers/3Dee.html. Proteins 2001; 42:332-344. (C) 2000 Wiley-Liss, Inc.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 27/11/20 alle ore 01:44:31