Computational analysis of the stability of SCF ligases employing domain information

Because of the unequivocally fundamental role of SCF ubiquitin ligase in many biological functions within a living cell including regulating DNA repair, cell cycle progression, and inflammation, we have analyzed the role of domain interactions in determining particular types of protein-protein interactions (PPIs) that are known or predicted to occur involving subunit components of the SCF-ligase complex. We focus on the prediction and analysis of obligate and non-obligate SCF-ligase complexes by using sequence domains from the Pfam database. After extracting different types of feature vectors, the prediction is performed via a support vector machine (SVM). The numerical results demonstrate that most of the interactions of SCF-ligase complexes are mediated by at least one domain. Moreover, domain-domain interactions dominate in obligate complexes whereas non-obligate complexes exhibit more domain-peptide chain interactions. Also, the computational results show that the best prediction accuracy of 80.46% is achieved using the combination of feature vectors of domain-domain type, domain-peptide chain type and no-domain interactions.