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Nucleic Acids Research Advance Access published online on October 21, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn785
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© 2008 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

InterPro: the integrative protein signature database

Sarah Hunter1,*, Rolf Apweiler1, Teresa K. Attwood2, Amos Bairoch3, Alex Bateman4, David Binns1, Peer Bork5, Ujjwal Das1, Louise Daugherty1, Lauranne Duquenne6, Robert D. Finn4, Julian Gough7, Daniel Haft8, Nicolas Hulo3, Daniel Kahn6, Elizabeth Kelly9, Aurélie Laugraud6, Ivica Letunic5, David Lonsdale1, Rodrigo Lopez1, Martin Madera7, John Maslen1, Craig McAnulla1, Jennifer McDowall1, Jaina Mistry4, Alex Mitchell1,2, Nicola Mulder9, Darren Natale10, Christine Orengo11, Antony F. Quinn1, Jeremy D. Selengut8, Christian J. A. Sigrist3, Manjula Thimma1, Paul D. Thomas12, Franck Valentin1, Derek Wilson13, Cathy H. Wu10 and Corin Yeats11

1EMBL Outstation European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, 2Faculty of Life Science and School of Computer Science, The University of Manchester, Manchester, UK, 3Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland, 4The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 5European Molecular Laboratory (EMBL), Heidelberg, Germany, 6Pole Rhone-Alpins de BioInformatique (PRABI) and Laboratoire de Biométrie et Biologie Evolutive, CNRS, INRIA, Université de Lyon, Université Lyon 1, Villeurbanne, France, 7Department of Computer Science, University of Bristol, Woodland Road, Bristol, UK, 8J. Craig Venter Institute (JCVI), Rockville, MD, 20850, USA, 9Computational Biology Unit, University of Cape Town, South Africa, 10Protein Information Resource (PIR), Georgetown University Medical Center, Washington, DC, USA, 11Department of Structural and Molecular Biology, University College London, London, UK, 12Evolutionary Systems Biology, SRI International, Menlo Park, CA, 94025-3493, USA and 13MRC Laboratory of Molecular Biology, Cambridge

*To whom correspondence should be addressed. Tel: +44 0 1223 494 481; Fax: +44 0 1223 494 468; Email: hunter{at}ebi.ac.uk

Received September 15, 2008. Revised October 8, 2008. Accepted October 9, 2008.

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total ~58 000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein–protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/).


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