A Protein-Protein Interaction Prediction Method Embracing Intra-Protein Domain Cohesion Information

Recently, many computational methods for predict-ing protein-protein interaction (PPI) have been devel-oped by utilizing domain-domain interaction or asso-ciated information. However, most of the methods lack of reflecting the collaboration effect of multiple do-mains to the prediction of PPI. In this paper, we devel-op a computational model that considers not only inter relationship between protein pair but also the intra-domain functional cohesion effect in PPI. In the com-putational model, a value assigning method to reflect the intra and inter collaboration devised and the com-puted values are stored in Interaction Significance (IS) matrix. Then an equation for PPI prediction is devised on IS matrix. For S. cerevisiae PPI data from DIP, MINT and IntAct, domain data from Pfam-A, the pre-diction method achieved 50.19 % and 84.57 % sensitivi-ty and specificity respectively. Here we also observed that embracing intra-domain effect gives positive result on PPI prediction by inspection of interaction proba-bility change in protein pairs