Release Notes

Release 11.0, Tuesday July 26th 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.Durbin (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), D.Peyruc (6), E.Quevillon (1), C.Sigrist (2), P.D.Thomas (14), C.H.Wu (10).

(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 UniProt, 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

Protein matches have been updated according to the latest update of UniProt and new methods from Gene3D, PANTHER, Pfam, PROSITE and TIGRFAMs, have been integrated.

  • Splice variants and their full-length parental sequence are now displayed in the Graphical Views.
  • ModBase models, annotated comparative protein structures with links to 1, are displayed in the Graphical Views as yellow/white striped bars. ModBase models are generated by the fully automated homology-modelling pipeline MODPIPE.

Contents and coverage of the current release

InterPro protein matches are now calculated for all UniProt proteins, which are a combination of UniProt/Swiss-Prot, UniProt/TrEMBL and PIR proteins. For more information see 1.

InterPro release 11.0 contains 12294 entries, representing 3240 domains, 8753 families, 230 repeats, 29 active sites, 21 binding sites and 21 post-translational modification sites. Overall, there are 8541364 InterPro hits from 1620653 UniProt protein sequences. A complete list is available from the ftp site.

DATABASE VERSION ENTRIES
SWISSPROT 47.4 188477
TrEMBL 30.4 1902258
PRINTS 37.0 1850
Pfam 17.0 7868
PROSITE patterns 19.3 1850
PROSITE preprofiles N/A 112
ProDom 2004.1 1522
InterPro 11.0 12294
Smart 4.0 663
TIGRFAMs 4.1 2454
PIRSF 2.68 1347
PANTHER 5.0 438
Superfamily 1.65 1160
GENE3D 3.0 117
GO Classification N/A 19150

92.0% of UniProt/Swiss-Prot - 173305 of 188477 proteins

76.1% of UniProt/TrEMBL - 1447348 of 1902258 proteins

77.5% of UniProt - 1620653 of 2090735 proteins

Last entry: IPR013019

20005 publications in PUBMED are referenced from InterPro.

Forthcoming changes

The next release of InterPro will be release 12.0 scheduled for October 2005. It will incorporate:

  • Links to IntAct
  • Improvements to the taxonomy, more detailed taxonomy and FASTA downloads
  • Additional reading, linked to abstracts
  • InterPro classification hierarchy based on GO terms