SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure
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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2018-12-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/23/12/3260 |
| _version_ | 1811232290200616960 |
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| author | Abdollah Dehzangi Yosvany López Ghazaleh Taherzadeh Alok Sharma Tatsuhiko Tsunoda |
| author_facet | Abdollah Dehzangi Yosvany López Ghazaleh Taherzadeh Alok Sharma Tatsuhiko Tsunoda |
| author_sort | Abdollah Dehzangi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T10:59:53Z |
| format | Article |
| id | doaj.art-19fa7b58c4524fb1aa45e21c7a2af0fa |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-04-12T10:59:53Z |
| publishDate | 2018-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-19fa7b58c4524fb1aa45e21c7a2af0fa2022-12-22T03:35:58ZengMDPI AGMolecules1420-30492018-12-012312326010.3390/molecules23123260molecules23123260SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary StructureAbdollah Dehzangi0Yosvany López1Ghazaleh Taherzadeh2Alok Sharma3Tatsuhiko Tsunoda4Department of Computer Science, Morgan State University, Baltimore, MD 21251, USAGenesis Institute of Genetic Research, Genesis Healthcare Co., Tokyo 150-6015, JapanSchool of Information and Communication Technology, Griffith University, Gold Coast 4222, AustraliaInstitute for Integrated and Intelligent Systems, Griffith University, Brisbane 4111, AustraliaLaboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, JapanPost 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.https://www.mdpi.com/1420-3049/23/12/3260post translational modificationsumoylationensemble classifierbaggingsecondary structureprofile-bigram |
| spellingShingle | Abdollah Dehzangi Yosvany López Ghazaleh Taherzadeh Alok Sharma Tatsuhiko Tsunoda SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure Molecules post translational modification sumoylation ensemble classifier bagging secondary structure profile-bigram |
| title | SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure |
| title_full | SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure |
| title_fullStr | SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure |
| title_full_unstemmed | SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure |
| title_short | SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure |
| title_sort | sumsec accurate prediction of sumoylation sites using predicted secondary structure |
| topic | post translational modification sumoylation ensemble classifier bagging secondary structure profile-bigram |
| url | https://www.mdpi.com/1420-3049/23/12/3260 |
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