Hany Alashwal and Safaai Deris and Razib M. Othman
Comparison of Domain and Hydrophobicity Features for the Prediction of ProteinProtein Interactions using Support Vector Machines
79 - 85
2007
1
7
International Journal of Biomedical and Biological Engineering
https://publications.waset.org/pdf/4070
https://publications.waset.org/vol/7
World Academy of Science, Engineering and Technology
The protein domain structure has been widely used as the most informative sequence feature to computationally predict proteinprotein interactions. However, in a recent study, a research group has reported a very high accuracy of 94 using hydrophobicity feature. Therefore, in this study we compare and verify the usefulness of protein domain structure and hydrophobicity properties as the sequence features. Using the Support Vector Machines (SVM) as the learning system, our results indicate that both features achieved accuracy of nearly 80. Furthermore, domains structure had receiver operating characteristic (ROC) score of 0.8480 with running time of 34 seconds, while hydrophobicity had ROC score of 0.8159 with running time of 20,571 seconds (5.7 hours). These results indicate that proteinprotein interaction can be predicted from domain structure with reliable accuracy and acceptable running time.
Open Science Index 7, 2007