Alashwal, Hany and Deris, Safaai and M. Othman, Razib (2007) Comparison of domain and hydrophobicity features for the prediction of protein-protein interactions using support vector machines. International Journal of Information Technology, 3 (1). pp. 18-24. ISSN 2070-3961
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Official URL: http://www.waset.org/ijit/
Abstract
The protein domain structure has been widely used as the most informative sequence feature to computationally predict protein-protein 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 protein-protein interaction can be predicted from domain structure with reliable accuracy and acceptable running time.
Item Type: | Article |
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Uncontrolled Keywords: | bioinformatics, protein-protein interactions, support vector machines, protein features |
Subjects: | Q Science > Q Science (General) Q Science > QA Mathematics > QA75 Electronic computers. Computer science |
Divisions: | Computer Science and Information System |
ID Code: | 8419 |
Deposited By: | Norshiela Buyamin |
Deposited On: | 04 May 2009 08:30 |
Last Modified: | 02 Jun 2010 01:55 |
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