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Bioinformatics 2005 21(Suppl 2):ii220-ii221; doi:10.1093/bioinformatics/bti1135
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

Decomposing protein networks into domain–domain interactions

Mario Albrecht 1,*, Carola Huthmacher 1, Silvio C. E. Tosatto 2 and Thomas Lengauer 1

1Max Planck Institute for Informatics Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany
2Department of Biology and CRIBI Biotechnology Center, University of Padova Viale G. Colombo 3, 35121 Padova, Italy

*To whom correspondence should be addressed.

Summary: The application of novel experimental techniques has generated large networks of protein–protein interactions. Frequently, important information on the structure and cellular function of protein–protein interactions can be gained from the domains of interacting proteins. We have designed a Cytoscape plugin that decomposes interacting proteins into their respective domains and computes a putative network of corresponding domain–domain interactions. To this end, the network graph of proteins has been extended by additional node and edge types for domain interactions, including different node and edge shapes and coloring schemes used for visualization. An additional plugin provides supplementary web links to Internet resources on domain function and structure.

Availability: Both Cytoscape plugins can be downloaded from http://www.cytoscape.org

Contact: mario.albrecht{at}mpi-inf.mpg.de


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