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This article is part of the supplement: Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Bioinformatics

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Inferring homologous protein-protein interactions through pair position specific scoring matrix

Chun-Yu Lin1, Yung-Chiang Chen1, Yu-Shu Lo and Jinn-Moon Yang12*

Author affiliations

1 Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan

2 Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan

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Citation and License

BMC Bioinformatics 2013, 14(Suppl 2):S11  doi:10.1186/1471-2105-14-S2-S11

Published: 21 January 2013



The protein-protein interaction (PPI) is one of the most important features to understand biological processes. For a PPI, the physical domain-domain interaction (DDI) plays the key role for biology functions. In the post-genomic era, to rapidly identify homologous PPIs for analyzing the contact residue pairs of their interfaces within DDIs on a genomic scale is essential to determine PPI networks and the PPI interface evolution across multiple species.


In this study, we proposed "pair

atrix (pairPSSM)" to identify homologous PPIs. The pairPSSM can successfully distinguish the true protein complexes from unreasonable protein pairs with about 90% accuracy. For the test set including 1,122 representative heterodimers and 2,708,746 non-interacting protein pairs, the mean average precision and mean false positive rate of pairPSSM were 0.42 and 0.31, respectively. Moreover, we applied pairPSSM to identify ~450,000 homologous PPIs with their interacting domains and residues in seven common organisms (e.g. Homo sapiens, Mus musculus, Saccharomyces cerevisiae and Escherichia coli).


Our pairPSSM is able to provide statistical significance of residue pairs using evolutionary profiles and a scoring system for inferring homologous PPIs. According to our best knowledge, the pairPSSM is the first method for searching homologous PPIs across multiple species using pair position specific scoring matrix and a 3D dimer as the template to map interacting domain pairs of these PPIs. We believe that pairPSSM is able to provide valuable insights for the PPI evolution and networks across multiple species.