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Literature DB >> 12520029

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

E V Kriventseva¹, F Servant, R Apweiler.

Abstract

The CluSTr database (http://www.ebi.ac.uk/clustr/) offers an automatic classification of SWISS-PROT+TrEMBL proteins into groups of related proteins. The clustering is based on analysis of all pair-wise sequence comparisons between proteins using the Smith-Waterman algorithm. The analysis, carried out on different levels of protein similarity, yields a hierarchical organization of clusters. Information about domain content of the clustered proteins is provided via the InterPro resource. The introduced InterPro 'condensed graphical view' simplifies the visual analysis of represented domain architectures. Integrated applications allow users to visualize and edit multiple alignments and build sequence divergence trees. Links to the relevant structural data in Protein Data Bank (PDB) and Homology derived Secondary Structure of Proteins (HSSP) are also provided.

Entities: Gene

Mesh：

Substances：
Proteins

Year: 2003 PMID： 12520029 PMCID： PMC165482 DOI： 10.1093/nar/gkg035

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

13 in total

1. A collection of well characterised integral membrane proteins.

Authors: S Möller; E V Kriventseva; R Apweiler
Journal: Bioinformatics Date: 2000-12 Impact factor: 6.937

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

Authors: E V Kriventseva; W Fleischmann; E M Zdobnov; R Apweiler
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

5. Significance of Z-value statistics of Smith-Waterman scores for protein alignments.

Authors: J P Comet; J C Aude; E Glémet; J L Risler; A Hénaut; P P Slonimski; J J Codani
Journal: Comput Chem Date: 1999-06-15

6. The Protein Data Bank: unifying the archive.

Authors: John Westbrook; Zukang Feng; Shri Jain; T N Bhat; Narmada Thanki; Veerasamy Ravichandran; Gary L Gilliland; Wolfgang Bluhm; Helge Weissig; Douglas S Greer; Philip E Bourne; Helen M Berman
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

7. The EBI SRS server-new features.

Authors: Evgeny M Zdobnov; Rodrigo Lopez; Rolf Apweiler; Thure Etzold
Journal: Bioinformatics Date: 2002-08 Impact factor: 6.937

8. 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

9. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.

Authors: Ada Hamosh; Alan F Scott; Joanna Amberger; Carol Bocchini; David Valle; Victor A McKusick
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

10. 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

12 in total

1. PHYTOPROT: a database of clusters of plant proteins.

Authors: S Mohseni-Zadeh; A Louis; P Brézellec; J-L Risler
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

2. Testing statistical significance scores of sequence comparison methods with structure similarity.

Authors: Tim Hulsen; Jacob de Vlieg; Jack A M Leunissen; Peter M A Groenen
Journal: BMC Bioinformatics Date: 2006-10-12 Impact factor: 3.169

3. SIMAP--structuring the network of protein similarities.

Authors: Thomas Rattei; Patrick Tischler; Roland Arnold; Franz Hamberger; Jörg Krebs; Jan Krumsiek; Benedikt Wachinger; Volker Stümpflen; Werner Mewes
Journal: Nucleic Acids Res Date: 2007-11-23 Impact factor: 16.971

4. JACOP: a simple and robust method for the automated classification of protein sequences with modular architecture.

Authors: Peter Sperisen; Marco Pagni
Journal: BMC Bioinformatics Date: 2005-08-31 Impact factor: 3.169

5. eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity.

Authors: Qiaojuan Jane Su; Lin Lu; Serge Saxonov; Douglas L Brutlag
Journal: Nucleic Acids Res Date: 2005-01-01 Impact factor: 16.971

6. Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.

Authors: Paul Kersey; Lawrence Bower; Lorna Morris; Alan Horne; Robert Petryszak; Carola Kanz; Alexander Kanapin; Ujjwal Das; Karine Michoud; Isabelle Phan; Alexandre Gattiker; Tamara Kulikova; Nadeem Faruque; Karyn Duggan; Peter Mclaren; Britt Reimholz; Laurent Duret; Simon Penel; Ingmar Reuter; Rolf Apweiler
Journal: Nucleic Acids Res Date: 2005-01-01 Impact factor: 16.971