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Literature DB >> 11125042

CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins.

E V Kriventseva¹, W Fleischmann, E M Zdobnov, R Apweiler.

Abstract

The CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. Analysis has been carried out for different levels of protein similarity, yielding a hierarchical organisation of clusters. The database provides links to InterPro, which integrates information on protein families, domains and functional sites from PROSITE, PRINTS, Pfam and ProDom. Links to the InterPro graphical interface allow users to see at a glance whether proteins from the cluster share particular functional sites. CluSTr also provides cross-references to HSSP and PDB. The database is available for querying and browsing at http://www.ebi.ac.uk/clustr.

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Year: 2001 PMID： 11125042 PMCID： PMC29804 DOI： 10.1093/nar/29.1.33

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

14 in total

1. PRINTS-S: the database formerly known as PRINTS.

Authors: T K Attwood; M D Croning; D R Flower; A P Lewis; J E Mabey; P Scordis; J N Selley; W Wright
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

2. The InterPro database, an integrated documentation resource for protein families, domains and functional sites.

Authors: R Apweiler; T K Attwood; A Bairoch; A Bateman; E Birney; M Biswas; P Bucher; L Cerutti; F Corpet; M D Croning; R Durbin; L Falquet; W Fleischmann; J Gouzy; H Hermjakob; N Hulo; I Jonassen; D Kahn; A Kanapin; Y Karavidopoulou; R Lopez; B Marx; N J Mulder; T M Oinn; M Pagni; F Servant; C J Sigrist; E M Zdobnov
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

3. Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.

Authors: R Apweiler; M Biswas; W Fleischmann; A Kanapin; Y Karavidopoulou; P Kersey; E V Kriventseva; V Mittard; N Mulder; I Phan; E Zdobnov
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

4. Removing redundancy in SWISS-PROT and TrEMBL.

Authors: C O'Donovan; M J Martin; E Glemet; J J Codani; R Apweiler
Journal: Bioinformatics Date: 1999-03 Impact factor: 6.937

5. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

Authors: A Bairoch; R Apweiler
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

6. Protein folds and families: sequence and structure alignments.

Authors: L Holm; C Sander
Journal: Nucleic Acids Res Date: 1999-01-01 Impact factor: 16.971

7. The PROSITE database, its status in 1999.

Authors: K Hofmann; P Bucher; L Falquet; A Bairoch
Journal: Nucleic Acids Res Date: 1999-01-01 Impact factor: 16.971

8. SRS: information retrieval system for molecular biology data banks.

Authors: T Etzold; A Ulyanov; P Argos
Journal: Methods Enzymol Date: 1996 Impact factor: 1.600

9. LASSAP, a LArge Scale Sequence compArison Package.

Authors: E Glémet; J J Codani
Journal: Comput Appl Biosci Date: 1997-04

10. Identification of common molecular subsequences.

Authors: T F Smith; M S Waterman
Journal: J Mol Biol Date: 1981-03-25 Impact factor: 5.469

33 in total

1. Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.

Review 2. EBI databases and services.

Authors: P Rodriguez-Tomé
Journal: Mol Biotechnol Date: 2001-07 Impact factor: 2.695

3. The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.

Authors: Evelyn Camon; Michele Magrane; Daniel Barrell; David Binns; Wolfgang Fleischmann; Paul Kersey; Nicola Mulder; Tom Oinn; John Maslen; Anthony Cox; Rolf Apweiler
Journal: Genome Res Date: 2003-03-12 Impact factor: 9.043

4. ProtoNet: hierarchical classification of the protein space.

Authors: Ori Sasson; Avishay Vaaknin; Hillel Fleischer; Elon Portugaly; Yonatan Bilu; Nathan Linial; Michal Linial
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

5. Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters.

Authors: E V Kriventseva; F Servant; R Apweiler
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

6. Protein families and TRIBES in genome sequence space.

Authors: Anton J Enright; Victor Kunin; Christos A Ouzounis
Journal: Nucleic Acids Res Date: 2003-08-01 Impact factor: 16.971

7. PANDORA: keyword-based analysis of protein sets by integration of annotation sources.

Authors: Noam Kaplan; Avishay Vaaknin; Michal Linial
Journal: Nucleic Acids Res Date: 2003-10-01 Impact factor: 16.971

8. Public web-based services from the European Bioinformatics Institute.

Authors: Nicola Harte; Ville Silventoinen; Emmanuel Quevillon; Stephen Robinson; Kimmo Kallio; Xavier Fustero; Pravin Patel; Petteri Jokinen; Rodrigo Lopez
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

9. Functional annotation prediction: all for one and one for all.

Authors: Ori Sasson; Noam Kaplan; Michal Linial
Journal: Protein Sci Date: 2006-05-02 Impact factor: 6.725

10. Database resources of the National Center for Biotechnology Information: 2002 update.

Authors: David L Wheeler; Deanna M Church; Alex E Lash; Detlef D Leipe; Thomas L Madden; Joan U Pontius; Gregory D Schuler; Lynn M Schriml; Tatiana A Tatusova; Lukas Wagner; Barbara A Rapp
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971