Nucleic Acids Research Advance Access originally published online on November 13, 2007
Nucleic Acids Research 2008 36(Database issue):D651-D655; doi:10.1093/nar/gkm996
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Nucleic Acids Research, 2008, Vol. 36, Database issue D651-D655
© 2007 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.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
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DIMA 2.0—predicted and known domain interactions
1Lehrstuhl für Genomorientierte Bioinformatik, Wissenschaftszentrum Weihenstephan, Technische Universität München, Am Forum 1, D-85350 Freising and 2Institute for Bioinformatics/MIPS, GSF – National Research Center for Environement and Health in the Helmholtz Association, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany
*To whom correspondence should be addressed. Tel: +49 8161 71 2131; Fax: +49 8161 71 2186; Email: p.pagel{at}wzw.tum.de
Received September 15, 2007. Revised October 20, 2007. Accepted October 22, 2007.
DIMA—the domain interaction map has evolved from a simple web server for domain phylogenetic profiling into an integrative prediction resource combining both experimental data on domain–domain interactions and predictions from two different algorithms. With this update, DIMA obtains greatly improved coverage at the level of genomes and domains as well as with respect to available prediction approaches. The domain phylogenetic profiling method now uses SIMAP as its backend for exhaustive domain hit coverage: 7038 Pfam domains were profiled over 460 completely sequenced genomes.Domain pair exclusion predictions were produced from 83 969 distinct protein–protein interactions obtained from IntAct resulting in 21 513 domain pairs with significant domain pair exclusion algorithm scores. Additional predictions applying the same algorithm to predicted protein interactions from STRING yielded 2378 high-confidence pairs. Experimental data comes from iPfam (3074) and 3did (3034 pairs), two databases identifying domain contacts in solved protein structures. Taken together, these two resources yielded 3653 distinct interacting domain pairs. DIMA is available at http://mips.gsf.de/genre/proj/dima.
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