Release Notes

Release 7.2, Monday March 29 2004

Acknowledgements

R.Apweiler (1), T.K.Attwood (4), A.Bairoch (2), A.Bateman (5), D.Binns (1), P.Bradley (1,4), P.Bork (8), P.Bucher (3), L. Cerutti (3), R.Copley (13), E.Courcelle (6), U.Das (1) R.Durbin (5), W.Fleischmann (1), J.Gough (11), J.Gouzy (6), S.Griffiths-Jones (5) D.Haft (9), N.Harte (1), N.Hulo (2), D.Kahn (6), A.Kanapin (1), M.Krestyaninova (1), D.Lonsdale (1), R.Lopez (1), I.Letunic (8), M.Madera (12), J.Maslen (1), J.McDowall (1), N.Mulder (1), A.N. Nikolskaya (10), S.Orchard (1), M.Pagni (3), D.Peyruc (6), C.Ponting (7), E.Quevillon (1), F.Servant (1), C.Sigrist (2), D.J.Studholme (5), 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) MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, 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) Department of Structural Biology School of Medicine, Stanford University, California, U.S.A;
(12) MRC Laboratory of Molecular Biology, Cambridge, UK.
(13) Wellcome Trust Centre for Human Genetics, Oxford, UK

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. SMART, TIGRFAMs, PIR SuperFamily and more recently SUPERFAMILY 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 UniProt. New methods from PIR SuperFamily, SUPERFAMILY, TIGRFAMs, and Pfam have been integrated.

Links from proteins to their corresponding PDB entries have been made and the protein structural chains are displayed in the graphical views as white and green striped bars. In the Detailed Graphical View the curated structural matches have been separated from InterPro matches, and are now listed at the bottom of the view. Links go to the MSD page of the appropriate PDB entries.

Links to MEROPS now include peptidase inhibitors as well as peptidases.

Contents of current release

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

InterPro release 7.2 contains 10709 entries, representing 2411 domains, 8035 families, 197 repeats, 26 active sites, 20 binding sites and 20 post-translational modification sites. Overall, there are 5382755 InterPro hits from 1216979 Swiss-Prot + TrEMBL protein sequences. A complete list is available from the ftp site.

The current version of InterPro consists of:

DATABASE VERSION ENTRIES
Swiss-Prot 42.11 146193
PRINTS 37.0 1850
TrEMBL 25.11 1070786
Pfam 12.0 7316
PROSITE patterns 18.10 1659
PROSITE preprofiles N/A 131
ProDom 2002.1 1021
InterPro 7.2 10709
Smart 4.0 663
TIGRFAMs 3.0 1977
PIR SuperFamily 2.41 219
SUPERFAMILY 1.63 552

Forthcoming changes

The next release of InterPro will be release 8.0 scheduled for June 2004. This will include new data from the member databases and further improvements to the Taxonomy servlet. In addition, work is underway to include extended predictions of structural class methods through CATH HMMs and to implement the InterPro Domain Architecture Viewer (IDA).