Method

Predicting domain-domain interactions using a parsimony approach

Katia S Guimarães^1,2 , Raja Jothi¹ , Elena Zotenko^1,3 and Teresa M Przytycka¹

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

²Center of Informatics, Federal University of Pernambuco, Recife, PE 50732, Brazil

³Department of Computer Science, University of Maryland, College Park, MD 20742, USA

author email corresponding author email

Genome Biology 2006, 7:R104doi:10.1186/gb-2006-7-11-r104

Published:	9 November 2006

Subject areas: Bioinformatics, Biochemistry and structural biology, Molecular biology

Abstract

We propose a novel approach to predict domain-domain interactions from a protein-protein interaction network. In our method we apply a parsimony-driven explanation of the network, where the domain interactions are inferred using linear programming optimization, and false positives in the protein network are handled by a probabilistic construction. This method outperforms previous approaches by a considerable margin. The results indicate that the parsimony principle provides a correct approach for detecting domain-domain contacts.