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Literature DB >> 14681377

Recent improvements to the PROSITE database.

Nicolas Hulo¹, Christian J A Sigrist, Virginie Le Saux, Petra S Langendijk-Genevaux, Lorenza Bordoli, Alexandre Gattiker, Edouard De Castro, Philipp Bucher, Amos Bairoch.

Abstract

The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or profiles. Each signature is linked to documentation that provides useful biological information on the protein family, domain or functional site identified by the signature. The PROSITE web page has been redesigned and several tools have been implemented to help the user discover new conserved regions in their own proteins and to visualize domain arrangements. We also introduced the facility to search PDB with a PROSITE entry or a user's pattern and visualize matched positions on 3D structures. The latest version of PROSITE (release 18.17 of November 30, 2003) contains 1676 entries. The database is accessible at http://www.expasy.org/prosite/.

Mesh：

Substances：
Proteins

Year: 2004 PMID： 14681377 PMCID： PMC308778 DOI： 10.1093/nar/gkh044

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

18 in total

1. The PROSITE database, its status in 2002.

Authors: Laurent Falquet; Marco Pagni; Philipp Bucher; Nicolas Hulo; Christian J A Sigrist; Kay Hofmann; Amos Bairoch
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

2. T-Coffee: A novel method for fast and accurate multiple sequence alignment.

Authors: C Notredame; D G Higgins; J Heringa
Journal: J Mol Biol Date: 2000-09-08 Impact factor: 5.469

3. UniProt: the Universal Protein knowledgebase.

Authors: Rolf Apweiler; Amos Bairoch; Cathy H Wu; Winona C Barker; Brigitte Boeckmann; Serenella Ferro; Elisabeth Gasteiger; Hongzhan Huang; Rodrigo Lopez; Michele Magrane; Maria J Martin; Darren A Natale; Claire O'Donovan; Nicole Redaschi; Lai-Su L Yeh
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

4. PRINTS and its automatic supplement, prePRINTS.

Authors: T K Attwood; P Bradley; D R Flower; A Gaulton; N Maudling; A L Mitchell; G Moulton; A Nordle; K Paine; P Taylor; A Uddin; C Zygouri
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

5. The InterPro Database, 2003 brings increased coverage and new features.

Authors: Nicola J Mulder; Rolf Apweiler; Teresa K Attwood; Amos Bairoch; Daniel Barrell; Alex Bateman; David Binns; Margaret Biswas; Paul Bradley; Peer Bork; Phillip Bucher; Richard R Copley; Emmanuel Courcelle; Ujjwal Das; Richard Durbin; Laurent Falquet; Wolfgang Fleischmann; Sam Griffiths-Jones; Daniel Haft; Nicola Harte; Nicolas Hulo; Daniel Kahn; Alexander Kanapin; Maria Krestyaninova; Rodrigo Lopez; Ivica Letunic; David Lonsdale; Ville Silventoinen; Sandra E Orchard; Marco Pagni; David Peyruc; Chris P Ponting; Jeremy D Selengut; Florence Servant; Christian J A Sigrist; Robert Vaughan; Evgueni M Zdobnov
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

6. PROSITE: a documented database using patterns and profiles as motif descriptors.

Authors: Christian J A Sigrist; Lorenzo Cerutti; Nicolas Hulo; Alexandre Gattiker; Laurent Falquet; Marco Pagni; Amos Bairoch; Philipp Bucher
Journal: Brief Bioinform Date: 2002-09 Impact factor: 11.622

7. ScanProsite: a reference implementation of a PROSITE scanning tool.

Authors: Alexandre Gattiker; Elisabeth Gasteiger; Amos Bairoch
Journal: Appl Bioinformatics Date: 2002

8. Profile analysis.

Authors: M Gribskov; R Lüthy; D Eisenberg
Journal: Methods Enzymol Date: 1990 Impact factor: 1.600

9. Protein structure comparison by alignment of distance matrices.

Authors: L Holm; C Sander
Journal: J Mol Biol Date: 1993-09-05 Impact factor: 5.469

10. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

Authors: J D Thompson; D G Higgins; T J Gibson
Journal: Nucleic Acids Res Date: 1994-11-11 Impact factor: 16.971

123 in total

1. UniProt: the Universal Protein knowledgebase.

2. 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

Review 3. 'Conserved hypothetical' proteins: prioritization of targets for experimental study.

Authors: Michael Y Galperin; Eugene V Koonin
Journal: Nucleic Acids Res Date: 2004-10-12 Impact factor: 16.971

4. Complete nucleotide sequence of the conjugative tetracycline resistance plasmid pFBAOT6, a member of a group of IncU plasmids with global ubiquity.

Authors: Glenn Rhodes; Julian Parkhill; Christine Bird; Kerrie Ambrose; Matthew C Jones; Geert Huys; Jean Swings; Roger W Pickup
Journal: Appl Environ Microbiol Date: 2004-12 Impact factor: 4.792