Universiti Teknologi Malaysia Institutional Repository

Comparison of domain and hydrophobicity features for the prediction of protein-protein interactions using support vector machines

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

[img]
Preview
PDF
362Kb

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
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 (Formerly known)
ID Code:8419
Deposited By: Norshiela Buyamin
Deposited On:04 May 2009 08:30
Last Modified:02 Jun 2010 01:55

Repository Staff Only: item control page