Release Notes

Release 12.0, Friday November 18th 2005

Acknowledgements

R.Apweiler (1), T.K.Attwood (4), A.Bairoch (2), A.Bateman (5), D.Binns (1), P.Bork (8), P.Bucher (3), M.J.Campbell (14), L.Cerutti (3), R.Copley (13), E.Courcelle (6), U.Das (1), L.Daugherty (1), M.Dibley (7), R.Finn (5), W.Fleischmann (1), J.Gough (11), D.Haft (9), N.Hulo (2), S.Hunter (1), D.Kahn (6), A.Kanapin (1), M.Krestyaninova (1), D.Lonsdale (1), R.Lopez (1), I.Letunic (8), M.Madera (12), J.Maslen (1), C.McAnulla (1), J.McDowall (1), J.Mistry (5), A.Mitchell (1,4), N.Mulder (1), A.N.Nikolskaya (10), S.Orchard (1), C.Orengo (7), M.Pagni (3), C.Sigrist (2), P.D.Thomas (14), D.Wison (12), C.H.Wu (10), C.Yates (7).

(1) EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK;
(2) Swiss Institute for Bioinformatics, Geneva, Switzerland;
(3) Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland;
(4) School of Biological Sciences, The University of Manchester, Manchester, UK;
(5) The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK;
(6) CNRS/INRA, Toulouse, France;
(7) Biochemistry and Molecular Biology Department, University College London, University of London, UK;
(8) Biocomputing Unit, EMBL-Heidelberg, Germany;
(9) The Institute for Genomic Research, Maryland, USA;
(10) Protein Information Resource, Georgetown University Medical Center, Washington, D.C., USA;
(11) Genomic Sciences Centre, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Japan;
(12) MRC Laboratory of Molecular Biology, Cambridge, UK;
(13) Wellcome Trust Centre for Human Genetics, Oxford, UK;
(14) Computational Biology, Applied Biosystems, 850 Lincoln Center Drive, Foster City, CA 94404, USA.

Current Release

Introduction

The databases Swiss-Prot and TrEMBL (now part of UniProtKB), PROSITE, PRINTS, Pfam and ProDom joined forces to launch an Integrated Documentation Resource of Protein Families, Domains and Functional Sites, abbreviated InterPro. Since then SMART, TIGRFAMs, PIRSF, SUPERFAMILY and more recently PANTHER and Gene3D, have joined InterPro. A detailed description of the project can be found in the user manual.

Changes since last release

The protein matches have been updated according to the latest update of UniProtKB and new methods from Gene3D, Pfam, PRINTS, PROSITE and SMART have been integrated

Contents and coverage of the current release

InterPro protein matches are now calculated for all UniProtKB proteins, which are a combination of UniProtKB/Swiss-Prot, UniProtKB/TrEMBL and PIR proteins. For more information see UniProtKB.

InterPro release 12.0 contains 12542 entries, representing 3289 domains, 8945 families, 234 repeats, 32 active sites, 21 binding sites and 21 post-translational modification sites. Overall, there are 10123516 InterPro hits from 1966591 UniProt protein sequences. A complete list is available from the ftp site.

DATABASE VERSION ENTRIES
SWISS-PROT 48.3 197228
PRINTS 38.0 1900
TrEMBL 31.3 2342938
Pfam 18.0 7973
PROSITE patterns 19.10 1882
PROSITE preprofiles N/A 109
ProDom 2004.1 1522
InterPro 12.0 12542
Smart 5.0 668
TIGRFAMs 4.1 2454
GO Classification N/A 20016
PIR SuperFamily 2.68 1347
PANTHER 5.0 438
Superfamily 1.65 1160
GENE3D 3.0 117

92.0% of UniProtKB/Swiss-Prot - 181542 of 197228 proteins

76.2% of UniProtKB/TrEMBL - 1785049 of 2342938 proteins

77.4% of UniProtKB - 1966591 of 2540166 proteins

Last entry: IPR013333

20692 publications in PUBMED are referenced from InterPro.

Forthcoming changes

The next release of InterPro will be release 12.1 scheduled for February 2006. It will incorporate: