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Nucleic Acids Research 2005 33(Database Issue):D201-D205; doi:10.1093/nar/gki106
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Nucleic Acids Research, 2005, Vol. 33, Database issue D201-D205
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

InterPro, progress and status in 2005

Nicola J. Mulder1,*, Rolf Apweiler1, Teresa K. Attwood3, Amos Bairoch4, Alex Bateman2, David Binns1, Paul Bradley1,3, Peer Bork5, Phillip Bucher6, Lorenzo Cerutti6, Richard Copley7, Emmanuel Courcelle8, Ujjwal Das1, Richard Durbin2, Wolfgang Fleischmann1, Julian Gough9, Daniel Haft10, Nicola Harte1, Nicolas Hulo4, Daniel Kahn8, Alexander Kanapin1, Maria Krestyaninova1, David Lonsdale1, Rodrigo Lopez1, Ivica Letunic5, Martin Madera11, John Maslen1, Jennifer McDowall1, Alex Mitchell1,3, Anastasia N. Nikolskaya12, Sandra Orchard1, Marco Pagni6, Chris P. Ponting13, Emmanuel Quevillon1, Jeremy Selengut10, Christian J. A. Sigrist4, Ville Silventoinen1, David J. Studholme2, Robert Vaughan1 and Cathy H. Wu12

1 EMBL Outstation—European Bioinformatics Institute and 2 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 3 School of Biological Sciences and Department of Computer Science, The University of Manchester, Manchester, UK, 4 Swiss Institute for Bioinformatics, Geneva, Switzerland, 5 Biocomputing Unit EMBL, Heidelberg, Germany, 6 Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland, 7 Wellcome Trust Centre for Human Genetics, Oxford, UK, 8 CNRS/INRA, Toulouse, France, 9 Genomic Sciences Centre, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Japan, 10 The Institute for Genomic Research, MD, USA, 11 MRC Laboratory of Molecular Biology, Cambridge, UK, 12 Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA and 13 MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford, UK

* To whom correspondence should be addressed. Tel: +44 0 1223 494 602; Fax: +44 0 1223 494 468; Email: mulder{at}ebi.ac.uk

Received September 20, 2004; Revised and Accepted October 18, 2004

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site. PIRSF and the structure-based SUPERFAMILY are the latest member databases to join InterPro, and CATH and PANTHER are soon to be integrated. InterPro release 8.0 contains 11 007 entries, representing 2573 domains, 8166 families, 201 repeats, 26 active sites, 21 binding sites and 20 post-translational modification sites. InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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 Nucleic Acids ResHome page
F. Al-Shahrour, P. Minguez, J. Tarraga, D. Montaner, E. Alloza, J. M. Vaquerizas, L. Conde, C. Blaschke, J. Vera, and J. Dopazo
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W472 - W476.
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 Appl. Environ. Microbiol.Home page
Q. He, K. H. Huang, Z. He, E. J. Alm, M. W. Fields, T. C. Hazen, A. P. Arkin, J. D. Wall, and J. Zhou
Energetic Consequences of Nitrite Stress in Desulfovibrio vulgaris Hildenborough, Inferred from Global Transcriptional Analysis.
Appl. Envir. Microbiol., June 1, 2006; 72(6): 4370 - 4381.
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 Microbiol. Mol. Biol. Rev.Home page
M.-J. Han and S. Y. Lee
The Escherichia coli Proteome: Past, Present, and Future Prospects
Microbiol. Mol. Biol. Rev., June 1, 2006; 70(2): 362 - 439.
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 MicrobiologyHome page
R. A. Slayden, D. L. Knudson, and J. T. Belisle
Identification of cell cycle regulators in Mycobacterium tuberculosis by inhibition of septum formation and global transcriptional analysis
Microbiology, June 1, 2006; 152(6): 1789 - 1797.
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