Release Notes

Release 7.0, Tues July 22 2003

http://www.ebi.ac.uk/interpro/
ftp://ftp.ebi.ac.uk/pub/databases/interpro/

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.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 SWISS-PROT, TrEMBL, 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 SuperFamilies and more recently SUPERFAMILY joined InterPro. A detailed description of the project can be found in the user manual.

Changes since last release

New methods from SUPERFAMILY, TIGRfams, Pfam and PROSITE have been integrated.

Links to COMe, the bioinorganic motif database have been made. COMe is an attempt to classify metalloproteins and some other complex proteins using the concept of bioinorganic motif. A bioinorganic motif (BIM) may be defined as a common structural feature of a class of functionally related, but not necessarily homologous, proteins, that includes the metal atom(s) and first coordination shell ligands.

Links to Merops have been introduced. Merops is database of peptidases and protein inhibitors. Only links to the peptidases are available in this release, it is hoped to incorporate Merops inhibitor families into InterPro in the next release.

The protein matches have been updated according to the latest updates of SWISS-PROT and TrEMBL. @@InterProScan has also been updated to include new member database signatures and SUPERFAMILY HMMs. A taxonomy servlet which was introduced in release 6.2 to display the taxonomic range of proteins matching an entry has been extended. The servlet now includes an extended taxonomy view of the protein matches and groups the protein matches according to their taxonomy. It is hoped that protein sequences retrieval capability in FASTA format for each taxonomic group will be implimented in the future.

Contents of current release

InterPro release 7.0 contains 8547 entries, representing 1902 domains, 6416 families, 163 repeats, 26 active sites, 20 binding sites and 20 post translational modifications. Overall, there are 4655236 InterPro hits from 1074041 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 42.5 138922
PRINTS 37.0 1850
TrEMBL 25.5 1013263
Pfam 11.0 7255
PROSITE patterns 18.10 1659
PROSITE preprofiles N/A 131
ProDom 2002.1 1021
InterPro 7.1 10383
Smart 3.4 654
TIGRFAMs 3.0 1977
PIR SuperFamily 2.0 100
Superfamily 1.63 552

Forthcoming changes

The next release of InterPro will be release 7.2 scheduled for March 2004. This will include new data from the member databases.@@

Feedback

We need your help and would welcome any feedback. If you find errors or omissions please let us know. You can contact us at: Interhelp@ebi.ac.uk.

Copyright

InterPro - Integrated Resource Of Protein Domains And Functional Sites. Copyright (C) 2001 The InterPro Consortium. This manual and the accompanying database may be copied and redistributed freely, without advance permission, provided that this Copyright statement is reproduced with each copy.