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Open AccessArticle

SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure

1
Department of Computer Science, Morgan State University, Baltimore, MD 21251, USA
2
Genesis Institute of Genetic Research, Genesis Healthcare Co., Tokyo 150-6015, Japan
3
School of Information and Communication Technology, Griffith University, Gold Coast 4222, Australia
4
Institute for Integrated and Intelligent Systems, Griffith University, Brisbane 4111, Australia
5
School of Engineering & Physics, University of the South Pacific, Suva, Fiji
6
Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
7
CREST, JST, Tokyo 102-0076, Japan
8
Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Molecules 2018, 23(12), 3260; https://doi.org/10.3390/molecules23123260
Received: 28 October 2018 / Revised: 30 November 2018 / Accepted: 5 December 2018 / Published: 10 December 2018
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. View Full-Text
Keywords: post translational modification; sumoylation; ensemble classifier; bagging; secondary structure; profile-bigram post translational modification; sumoylation; ensemble classifier; bagging; secondary structure; profile-bigram
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Dehzangi, A.; López, Y.; Taherzadeh, G.; Sharma, A.; Tsunoda, T. SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure. Molecules 2018, 23, 3260.

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