Prediction of post-translational modification sites using multiple kernel support vector machine
Protein post-translational modification (PTM) is an important mechanism that is involved in the regulation of protein function. Considering the high-cost and labor-intensive of experimental identification, many computational prediction methods are currently available for the prediction of PTM sites...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2017-04-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/3261.pdf |
| _version_ | 1797423869238181888 |
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| author | BingHua Wang Minghui Wang Ao Li |
| author_facet | BingHua Wang Minghui Wang Ao Li |
| author_sort | BingHua Wang |
| collection | DOAJ |
| description | Protein post-translational modification (PTM) is an important mechanism that is involved in the regulation of protein function. Considering the high-cost and labor-intensive of experimental identification, many computational prediction methods are currently available for the prediction of PTM sites by using protein local sequence information in the context of conserved motif. Here we proposed a novel computational method by using the combination of multiple kernel support vector machines (SVM) for predicting PTM sites including phosphorylation, O-linked glycosylation, acetylation, sulfation and nitration. To largely make use of local sequence information and site-modification relationships, we developed a local sequence kernel and Gaussian interaction profile kernel, respectively. Multiple kernels were further combined to train SVM for efficiently leveraging kernel information to boost predictive performance. We compared the proposed method with existing PTM prediction methods. The experimental results revealed that the proposed method performed comparable or better performance than the existing prediction methods, suggesting the feasibility of the developed kernels and the usefulness of the proposed method in PTM sites prediction. |
| first_indexed | 2024-03-09T07:53:59Z |
| format | Article |
| id | doaj.art-d58278f75a43424facb5253c52f4d196 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:53:59Z |
| publishDate | 2017-04-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-d58278f75a43424facb5253c52f4d1962023-12-03T01:21:08ZengPeerJ Inc.PeerJ2167-83592017-04-015e326110.7717/peerj.3261Prediction of post-translational modification sites using multiple kernel support vector machineBingHua Wang0Minghui Wang1Ao Li2University of Science and Technology of China, School of Information Science and Technology, Hefei, ChinaUniversity of Science and Technology of China, School of Information Science and Technology, Hefei, ChinaUniversity of Science and Technology of China, School of Information Science and Technology, Hefei, ChinaProtein post-translational modification (PTM) is an important mechanism that is involved in the regulation of protein function. Considering the high-cost and labor-intensive of experimental identification, many computational prediction methods are currently available for the prediction of PTM sites by using protein local sequence information in the context of conserved motif. Here we proposed a novel computational method by using the combination of multiple kernel support vector machines (SVM) for predicting PTM sites including phosphorylation, O-linked glycosylation, acetylation, sulfation and nitration. To largely make use of local sequence information and site-modification relationships, we developed a local sequence kernel and Gaussian interaction profile kernel, respectively. Multiple kernels were further combined to train SVM for efficiently leveraging kernel information to boost predictive performance. We compared the proposed method with existing PTM prediction methods. The experimental results revealed that the proposed method performed comparable or better performance than the existing prediction methods, suggesting the feasibility of the developed kernels and the usefulness of the proposed method in PTM sites prediction.https://peerj.com/articles/3261.pdfPost-translational modificationMultiple kernelsGaussian interaction profile kernel |
| spellingShingle | BingHua Wang Minghui Wang Ao Li Prediction of post-translational modification sites using multiple kernel support vector machine PeerJ Post-translational modification Multiple kernels Gaussian interaction profile kernel |
| title | Prediction of post-translational modification sites using multiple kernel support vector machine |
| title_full | Prediction of post-translational modification sites using multiple kernel support vector machine |
| title_fullStr | Prediction of post-translational modification sites using multiple kernel support vector machine |
| title_full_unstemmed | Prediction of post-translational modification sites using multiple kernel support vector machine |
| title_short | Prediction of post-translational modification sites using multiple kernel support vector machine |
| title_sort | prediction of post translational modification sites using multiple kernel support vector machine |
| topic | Post-translational modification Multiple kernels Gaussian interaction profile kernel |
| url | https://peerj.com/articles/3261.pdf |
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