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This article is part of the supplement: Selected articles from the Twelfth Asia Pacific Bioinformatics Conference (APBC 2014): Genomics

Open Access Proceedings

Cluster based prediction of PDZ-peptide interactions

Kousik Kundu1 and Rolf Backofen1234*

Author Affiliations

1 Bioinformatics Group, Department of Computer Science, University of Freiburg, Germany

2 Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Germany

3 Centre for Biological Systems Analysis (ZBSA), University of Freiburg, Germany

4 Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark

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BMC Genomics 2014, 15(Suppl 1):S5  doi:10.1186/1471-2164-15-S1-S5

Published: 24 January 2014

Abstract

Background

PDZ domains are one of the most promiscuous protein recognition modules that bind with short linear peptides and play an important role in cellular signaling. Recently, few high-throughput techniques (e.g. protein microarray screen, phage display) have been applied to determine in-vitro binding specificity of PDZ domains. Currently, many computational methods are available to predict PDZ-peptide interactions but they often provide domain specific models and/or have a limited domain coverage.

Results

Here, we composed the largest set of PDZ domains derived from human, mouse, fly and worm proteomes and defined binding models for PDZ domain families to improve the domain coverage and prediction specificity. For that purpose, we first identified a novel set of 138 PDZ families, comprising of 548 PDZ domains from aforementioned organisms, based on efficient clustering according to their sequence identity. For 43 PDZ families, covering 226 PDZ domains with available interaction data, we built specialized models using a support vector machine approach. The advantage of family-wise models is that they can also be used to determine the binding specificity of a newly characterized PDZ domain with sufficient sequence identity to the known families. Since most current experimental approaches provide only positive data, we have to cope with the class imbalance problem. Thus, to enrich the negative class, we introduced a powerful semi-supervised technique to generate high confidence non-interaction data. We report competitive predictive performance with respect to state-of-the-art approaches.

Conclusions

Our approach has several contributions. First, we show that domain coverage can be increased by applying accurate clustering technique. Second, we developed an approach based on a semi-supervised strategy to get high confidence negative data. Third, we allowed high order correlations between the amino acid positions in the binding peptides. Fourth, our method is general enough and will easily be applicable to other peptide recognition modules such as SH2 domains and finally, we performed a genome-wide prediction for 101 human and 102 mouse PDZ domains and uncovered novel interactions with biological relevance. We make all the predictive models and genome-wide predictions freely available to the scientific community.

Keywords:
PDZ domain-peptide interactions; protein recognition modules; protein domain clustering; semi-supervised learning; support vector machines