Dehzangi, Abdollah and Lopez, Yosvany and Taherzadeh, Ghazaleh and Sharma, Alokanand and Tsunoda, Tatsuhiko (2018) SumSec: accurate prediction of Sumoylation sites using predicted secondary structure. Molecules, 23 (12). pp. 1-13. ISSN 1420-3049
Preview |
PDF
- Published Version
Download (1MB) | Preview |
Abstract
Post Translational Modification (PTM) is defined as the modification of amino acids along the protein sequences after the translation process. These modifications significantly impact on the functioning of proteins. Therefore, having a comprehensive understanding of the underlying mechanism of PTMs turns out to be critical in studying the biological roles of proteins. Among a wide range of PTMs, sumoylation is one of the most important modifications due to its known cellular functions which include transcriptional regulation, protein stability, and protein subcellular localization. Despite its importance, determining sumoylation sites via experimental methods is time-consuming and costly. This has led to a great demand for the development of fast computational methods able to accurately determine sumoylation sites in proteins. In this study, we present a new machine learning-based method for predicting sumoylation sites called SumSec. To do this, we employed the predicted secondary structure of amino acids to extract two types of structural features from neighboring amino acids along the protein sequence which has never been used for this task. As a result, our proposed method is able to enhance the sumoylation site prediction task, outperforming previously proposed methods in the literature. SumSec demonstrated high sensitivity (0.91), accuracy (0.94) and MCC (0.88). The prediction accuracy achieved in this study is 21% better than those reported in previous studies. The script and extracted features are publicly available at: https://github.com/YosvanyLopez/SumSec.
| Item Type: | Journal Article |
|---|---|
| Subjects: | Q Science > Q Science (General) T Technology > T Technology (General) |
| Divisions: | Faculty of Science, Technology and Environment (FSTE) > School of Engineering and Physics |
| Depositing User: | Alokanand Sharma |
| Date Deposited: | 20 Feb 2019 00:44 |
| Last Modified: | 20 Feb 2019 00:44 |
| URI: | https://repository.usp.ac.fj/id/eprint/11320 |
Actions (login required)
 |
View Item |