Comparison of domain and hydrophobicity features for the prediction of protein-protein interactions using support vector machines
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...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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World Academy of Science, Engineering and Technology
2007
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| Subjects: | |
| Online Access: | http://eprints.utm.my/8419/ http://eprints.utm.my/8419/1/HAlashwal2007-Comparison_of_Domain_and_Hydrophobicity.pdf |
| _version_ | 1848891683550265344 |
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| author | Alashwal, Hany Deris, Safaai M. Othman, Razib |
| author_facet | Alashwal, Hany Deris, Safaai M. Othman, Razib |
| author_sort | Alashwal, Hany |
| building | UTeM Institutional Repository |
| collection | Online Access |
| description | 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.
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| first_indexed | 2025-11-15T21:01:52Z |
| format | Article |
| id | utm-8419 |
| institution | Universiti Teknologi Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T21:01:52Z |
| publishDate | 2007 |
| publisher | World Academy of Science, Engineering and Technology |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | utm-84192010-06-02T01:55:03Z http://eprints.utm.my/8419/ Comparison of domain and hydrophobicity features for the prediction of protein-protein interactions using support vector machines Alashwal, Hany Deris, Safaai M. Othman, Razib Q Science (General) QA75 Electronic computers. Computer science 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. World Academy of Science, Engineering and Technology 2007 Article PeerReviewed application/pdf en http://eprints.utm.my/8419/1/HAlashwal2007-Comparison_of_Domain_and_Hydrophobicity.pdf 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 http://www.waset.org/ijit/ |
| spellingShingle | Q Science (General) QA75 Electronic computers. Computer science Alashwal, Hany Deris, Safaai M. Othman, Razib Comparison of domain and hydrophobicity features for the prediction of protein-protein interactions using support vector machines |
| title | Comparison of domain and hydrophobicity features for the prediction of protein-protein interactions using support vector machines
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| title_full | Comparison of domain and hydrophobicity features for the prediction of protein-protein interactions using support vector machines
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| title_fullStr | Comparison of domain and hydrophobicity features for the prediction of protein-protein interactions using support vector machines
|
| title_full_unstemmed | Comparison of domain and hydrophobicity features for the prediction of protein-protein interactions using support vector machines
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| title_short | Comparison of domain and hydrophobicity features for the prediction of protein-protein interactions using support vector machines
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| title_sort | comparison of domain and hydrophobicity features for the prediction of protein-protein interactions using support vector machines |
| topic | Q Science (General) QA75 Electronic computers. Computer science |
| url | http://eprints.utm.my/8419/ http://eprints.utm.my/8419/ http://eprints.utm.my/8419/1/HAlashwal2007-Comparison_of_Domain_and_Hydrophobicity.pdf |