Protein-Protein Interaction Prediction

Interactions among proteins are essential to many biological functions in living cells but experimentally detected interactions represent only a small fraction of the real interaction network. Computational protein interaction prediction methods have become important to augment the experimental methods; in particular sequence based prediction methods that do not require additional data such as homologous sequences or 3D structure information which are often not available. Our  algorithm, termed Protein Interaction Prediction Engine (PIPE), falls into this category. Parkhas compared our method with other methods and concluded that our method “significantly outperforms the others in terms of recall-precision across both the yeast and human data”⁠. Our parallel PIPE algorithm allowed us to perform the first ever scan of the entire S. cerevisiae (yeast)  and Homo sapiens (human) proteomes. Several previously unknown protein interactions that we predicted have later been experimentally verified.



  • S.Pitre, M.Hooshyar, A.Schoenrock, B.Samanfar, M.Jessulat, J.R.Green, F.Dehne, A.Golshani, "Short co-occurring polypeptide regions can predict global protein interaction maps”, Scientific Reports (Nature.com/srep), vol.2, art.239, 2012. [pdf |link | pubmed]

  • A.Schoenrock, F.Dehne, J.R.Green, A.Golshani, S.Pitre, “MP-PIPE: A Massively Parallel Protein-Protein Interaction Prediction Engine”, in Proc. Int. Conf. on Supercomputing (ICS '11), pp.327-337, ACM Dig. Library, 2011. [pdf | link]

  • S.Pitre*, C.North*, M.Alamgir, M.Jessulat, A.Chan, X.Luo, J.R. Green, M.Dumontier, F.Dehne*, and A.Golshani*, "Global investigation of protein–protein interactions in yeast saccharomyces cerevisiae using re-occurring short polypeptide sequences", Nucleic Acids Research, vol.36, pp.4286-4294, 2008. [pdf | link | pubmed]

  • S.Pitre*, F.Dehne*, A.Chan, J.Cheetham, A.Duong, A.Emili, M.Gebbia, J.Greenblatt, M.Jessulat, N.Krogan, X.Luo, and A.Golshani*, "PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs", BMC Bioinformatics, vol.7, p.365 (15 pages), 2006. [pdf | link | pubmed]

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