Skip Navigation



Nucleic Acids Research Advance Access published online on November 14, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm977
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (4804K) Freely available
Right arrow Screen PDF (631K) Freely available
Right arrowOA All Versions of this Article:
36/suppl_1/D245    most recent
gkm977v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Hulo, N.
Right arrow Articles by Sigrist, C. J. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hulo, N.
Right arrow Articles by Sigrist, C. J. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007
The Author(s) 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.

Database Issue

The 20 years of PROSITE

Nicolas Hulo1,*, Amos Bairoch1,2, Virginie Bulliard1, Lorenzo Cerutti3, Béatrice A. Cuche1, Edouard de Castro1, Corinne Lachaize1, Petra S. Langendijk-Genevaux1 and Christian J. A. Sigrist1

1Swiss Institute of Bioinformatics (SIB), Centre Medical Universitaire, 2Structural Biology and Bioinformatics Department, University of Geneva, 1 rue Michel Servet, CH-1211 Geneva 4 and 3Swiss Institute of Bioinformatics (SIB), Génopode, UNIL-Sorge, CH-1015 Lausanne, Switzerland

*To whom correspondence should be addressed: Tel: +4122 379 58 72; Fax: +4122 379 58 58; Email: Nicolas.Hulo{at}isb-sib.ch

Received September 14, 2007. Revised October 17, 2007. Accepted October 18, 2007.

PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. In this article, we describe the implementation of a new method to assign a status to pattern matches, the new PROSITE web page and a new approach to improve the specificity and sensitivity of PROSITE methods. The latest version of PROSITE (release 20.19 of 11 September 2007) contains 1319 patterns, 745 profiles and 764 ProRules. Over the past 2 years, about 200 domains have been added, and now 53% of UniProtKB/Swiss-Prot entries (release 54.2 of 11 September 2007) have a PROSITE match. PROSITE is available on the web at: http://www.expasy.org/prosite/.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Virol.Home page
R. M. Presti, G. Zhao, W. L. Beatty, K. A. Mihindukulasuriya, A. P. A. Travassos da Rosa, V. L. Popov, R. B. Tesh, H. W. Virgin, and D. Wang
Quaranfil, Johnston Atoll, and Lake Chad Viruses Are Novel Members of the Family Orthomyxoviridae
J. Virol., November 15, 2009; 83(22): 11599 - 11606.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Marsico, K. Scheubert, A. Tuukkanen, A. Henschel, C. Winter, R. Winnenburg, and M. Schroeder
MeMotif: a database of linear motifs in {alpha}-helical transmembrane proteins
Nucleic Acids Res., November 12, 2009; (2009) gkp1042v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. J. A. Sigrist, L. Cerutti, E. de Castro, P. S. Langendijk-Genevaux, V. Bulliard, A. Bairoch, and N. Hulo
PROSITE, a protein domain database for functional characterization and annotation
Nucleic Acids Res., October 25, 2009; (2009) gkp885v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Velankar, C. Best, B. Beuth, C. H. Boutselakis, N. Cobley, A. W. Sousa Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, et al.
PDBe: Protein Data Bank in Europe
Nucleic Acids Res., October 25, 2009; (2009) gkp916v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Mihara, T. Itoh, and T. Izawa
SALAD database: a motif-based database of protein annotations for plant comparative genomics
Nucleic Acids Res., October 23, 2009; (2009) gkp831v1.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
L. Viljakainen, J. D. Evans, M. Hasselmann, O. Rueppell, S. Tingek, and P. Pamilo
Rapid Evolution of Immune Proteins in Social Insects
Mol. Biol. Evol., August 1, 2009; 26(8): 1791 - 1801.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. S. Ooi, C. Y. Kwo, M. Wildpaner, F. L. Sirota, B. Eisenhaber, S. Maurer-Stroh, W. C. Wong, A. Schleiffer, F. Eisenhaber, and G. Schneider
ANNIE: integrated de novo protein sequence annotation
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W435 - W440.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
M. Sandoval-Calderon, O. Geiger, Z. Guan, F. Barona-Gomez, and C. Sohlenkamp
A Eukaryote-like Cardiolipin Synthase Is Present in Streptomyces coelicolor and in Most Actinobacteria
J. Biol. Chem., June 26, 2009; 284(26): 17383 - 17390.
[Abstract] [Full Text] [PDF]

Home page
 J. Gen. Virol.Home page
E. Schulz, M. Gottschling, I. G. Bravo, U. Wittstatt, E. Stockfleth, and I. Nindl
Genomic characterization of the first insectivoran papillomavirus reveals an unusually long, second non-coding region and indicates a close relationship to Betapapillomavirus
J. Gen. Virol., March 1, 2009; 90(3): 626 - 633.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
E. Lang, K. Haugen, B. Fleckenstein, H. Homberset, S. A. Frye, O. H. Ambur, and T. Tonjum
Identification of neisserial DNA binding components
Microbiology, March 1, 2009; 155(3): 852 - 862.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
L. Chatre, L. A. Matheson, A. S. Jack, S. L. Hanton, and F. Brandizzi
Efficient mitochondrial targeting relies on co-operation of multiple protein signals in plants
J. Exp. Bot., March 1, 2009; 60(3): 741 - 749.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
A. Wilczynska, N. Minshall, J. Armisen, E. A. Miska, and N. Standart
Two Piwi proteins, Xiwi and Xili, are expressed in the Xenopus female germline
RNA, February 1, 2009; 15(2): 337 - 345.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
J. Mulvenna, B. Hamilton, S. H. Nagaraj, D. Smyth, A. Loukas, and J. J. Gorman
Proteomics Analysis of the Excretory/Secretory Component of the Blood-feeding Stage of the Hookworm, Ancylostoma caninum
Mol. Cell. Proteomics, January 1, 2009; 8(1): 109 - 121.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. P. Davis, C. G. Murphy, C. A. Saraceni-Richards, M. C. Rosenstein, T. C. Wiegers, and C. J. Mattingly
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D786 - D792.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
O. D. Testa, E. Moutevelis, and D. N. Woolfson
CC+: a relational database of coiled-coil structures
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D315 - D322.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Lima, A. H. Auchincloss, E. Coudert, G. Keller, K. Michoud, C. Rivoire, V. Bulliard, E. de Castro, C. Lachaize, D. Baratin, et al.
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D471 - D478.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Koua, L. Cerutti, L. Falquet, C. J. A. Sigrist, G. Theiler, N. Hulo, and C. Dunand
PeroxiBase: a database with new tools for peroxidase family classification
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D261 - D266.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Fukuchi, K. Homma, S. Sakamoto, H. Sugawara, Y. Tateno, T. Gojobori, and K. Nishikawa
The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D333 - D337.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. J. Richardson, Q. Gao, C. Mitsopoulous, M. Zvelebil, L. H. Pearl, and F. M. G. Pearl
MoKCa database--mutations of kinases in cancer
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D824 - D831.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. M. Berman, J. D. Westbrook, M. J. Gabanyi, W. Tao, R. Shah, A. Kouranov, T. Schwede, K. Arnold, F. Kiefer, L. Bordoli, et al.
The protein structure initiative structural genomics knowledgebase
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D365 - D368.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
M. Robertson, C. A. Helliwell, and E. S. Dennis
Post-Translational Modifications of the Endogenous and Transgenic FLC Protein in Arabidopsis thaliana
Plant Cell Physiol., December 1, 2008; 49(12): 1859 - 1866.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Biol. CellHome page
D. Komander, M. Patel, M. Laurin, N. Fradet, A. Pelletier, D. Barford, and J.-F. Cote
An {alpha}-Helical Extension of the ELMO1 Pleckstrin Homology Domain Mediates Direct Interaction to DOCK180 and Is Critical in Rac Signaling
Mol. Biol. Cell, November 1, 2008; 19(11): 4837 - 4851.
[Abstract] [Full Text] [PDF]

Home page
 Sci SignalHome page
M. L. Miller, L. J. Jensen, F. Diella, C. Jorgensen, M. Tinti, L. Li, M. Hsiung, S. A. Parker, J. Bordeaux, T. Sicheritz-Ponten, et al.
Linear Motif Atlas for Phosphorylation-Dependent Signaling
Sci. Signal., September 2, 2008; 1(35): ra2 - ra2.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. J. Rigden and M. Y. Galperin
Sequence analysis of GerM and SpoVS, uncharacterized bacterial 'sporulation' proteins with widespread phylogenetic distribution
Bioinformatics, August 15, 2008; 24(16): 1793 - 1797.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
S. B. Quintaje and S. Orchard
The Annotation of Both Human and Mouse Kinomes in UniProtKB/Swiss-Prot: One Small Step in Manual Annotation, One Giant Leap for Full Comprehension of Genomes
Mol. Cell. Proteomics, August 1, 2008; 7(8): 1409 - 1419.
[Abstract] [Full Text] [PDF]

Home page
 Brief Funct Genomic ProteomicHome page
P. F. Gherardini and M. Helmer-Citterich
Structure-based function prediction: approaches and applications
Brief Funct Genomic Proteomic, July 3, 2008; (2008) eln030v1.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.