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Bioinformatics Advance Access published online on February 15, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl050
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 10, 2005
Revised January 16, 2006
Accepted February 7, 2006

Applications note

The DIMA web resource - exploring the protein domain network

Philipp Pagel 1 * {dagger}, Matthias Oesterheld 2 {dagger}, Volker Stümpflen 2, and Dmitrij Frishman 1

1 Department of Genome Oriented Bioinformatics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany; Institute for Bioinformatics/MIPS, GSF - Research Center for Environment and Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
2 Institute for Bioinformatics/MIPS, GSF - Research Center for Environment and Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany

* To whom correspondence should be addressed.
Philipp Pagel, E-mail: p.pagel{at}gsf.de


  Abstract

Summary: Conserved domains represent essential building blocks of most known proteins. Due to their role as modular components carrying out specific functions they form a network based both on functional relations and direct physical interactions. We have previously shown that domain interaction networks provide substantially novel information with respect to networks built on full-length protein chains. In this work we present a comprehensive web resource for exploring the Domain Interaction MAp (DIMA), interactively. The tool aims at integration of multiple data sources and prediction techniques, two of which have been implemented so far: domain phylogenetic profiling and experimentally demonstrated domain contacts from known three-dimensional structures. A powerful yet simple user interface enables the user to compute, visualize, navigate and download domain networks based on specific search criteria.

Availability: http://mips.gsf.de/genre/proj/dima.

Associate Editor: Christos Ouzounis

{dagger}These authors contributed equally to this work


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