SVM-SulfoSite: A support vector machine based predictor for sulfenylation sites

Abstract Protein S-sulfenylation, which results from oxidation of free thiols on cysteine residues, has recently emerged as an important post-translational modification that regulates the structure and function of proteins involved in a variety of physiological and pathological processes. By alterin...

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Autores principales:	Hussam J. AL-barakati, Evan W. McConnell, Leslie M. Hicks, Leslie B. Poole, Robert H. Newman, Dukka B. KC
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a2f299fb10184e2fa23fde2539f4dae7
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spelling	oai:doaj.org-article:a2f299fb10184e2fa23fde2539f4dae72021-12-02T15:07:59ZSVM-SulfoSite: A support vector machine based predictor for sulfenylation sites10.1038/s41598-018-29126-x2045-2322https://doaj.org/article/a2f299fb10184e2fa23fde2539f4dae72018-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-29126-xhttps://doaj.org/toc/2045-2322Abstract Protein S-sulfenylation, which results from oxidation of free thiols on cysteine residues, has recently emerged as an important post-translational modification that regulates the structure and function of proteins involved in a variety of physiological and pathological processes. By altering the size and physiochemical properties of modified cysteine residues, sulfenylation can impact the cellular function of proteins in several different ways. Thus, the ability to rapidly and accurately identify putative sulfenylation sites in proteins will provide important insights into redox-dependent regulation of protein function in a variety of cellular contexts. Though bottom-up proteomic approaches, such as tandem mass spectrometry (MS/MS), provide a wealth of information about global changes in the sulfenylation state of proteins, MS/MS-based experiments are often labor-intensive, costly and technically challenging. Therefore, to complement existing proteomic approaches, researchers have developed a series of computational tools to identify putative sulfenylation sites on proteins. However, existing methods often suffer from low accuracy, specificity, and/or sensitivity. In this study, we developed SVM-SulfoSite, a novel sulfenylation prediction tool that uses support vector machines (SVM) to identify key determinants of sulfenylation among five feature classes: binary code, physiochemical properties, k-space amino acid pairs, amino acid composition and high-quality physiochemical indices. Using 10-fold cross-validation, SVM-SulfoSite achieved 95% sensitivity and 83% specificity, with an overall accuracy of 89% and Matthew’s correlation coefficient (MCC) of 0.79. Likewise, using an independent test set of experimentally identified sulfenylation sites, our method achieved scores of 74%, 62%, 80% and 0.42 for accuracy, sensitivity, specificity and MCC, with an area under the receiver operator characteristic (ROC) curve of 0.81. Moreover, in side-by-side comparisons, SVM-SulfoSite performed as well as or better than existing sulfenylation prediction tools. Together, these results suggest that our method represents a robust and complementary technique for advanced exploration of protein S-sulfenylation.Hussam J. AL-barakatiEvan W. McConnellLeslie M. HicksLeslie B. PooleRobert H. NewmanDukka B. KCNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-9 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hussam J. AL-barakati Evan W. McConnell Leslie M. Hicks Leslie B. Poole Robert H. Newman Dukka B. KC SVM-SulfoSite: A support vector machine based predictor for sulfenylation sites
description	Abstract Protein S-sulfenylation, which results from oxidation of free thiols on cysteine residues, has recently emerged as an important post-translational modification that regulates the structure and function of proteins involved in a variety of physiological and pathological processes. By altering the size and physiochemical properties of modified cysteine residues, sulfenylation can impact the cellular function of proteins in several different ways. Thus, the ability to rapidly and accurately identify putative sulfenylation sites in proteins will provide important insights into redox-dependent regulation of protein function in a variety of cellular contexts. Though bottom-up proteomic approaches, such as tandem mass spectrometry (MS/MS), provide a wealth of information about global changes in the sulfenylation state of proteins, MS/MS-based experiments are often labor-intensive, costly and technically challenging. Therefore, to complement existing proteomic approaches, researchers have developed a series of computational tools to identify putative sulfenylation sites on proteins. However, existing methods often suffer from low accuracy, specificity, and/or sensitivity. In this study, we developed SVM-SulfoSite, a novel sulfenylation prediction tool that uses support vector machines (SVM) to identify key determinants of sulfenylation among five feature classes: binary code, physiochemical properties, k-space amino acid pairs, amino acid composition and high-quality physiochemical indices. Using 10-fold cross-validation, SVM-SulfoSite achieved 95% sensitivity and 83% specificity, with an overall accuracy of 89% and Matthew’s correlation coefficient (MCC) of 0.79. Likewise, using an independent test set of experimentally identified sulfenylation sites, our method achieved scores of 74%, 62%, 80% and 0.42 for accuracy, sensitivity, specificity and MCC, with an area under the receiver operator characteristic (ROC) curve of 0.81. Moreover, in side-by-side comparisons, SVM-SulfoSite performed as well as or better than existing sulfenylation prediction tools. Together, these results suggest that our method represents a robust and complementary technique for advanced exploration of protein S-sulfenylation.
format	article
author	Hussam J. AL-barakati Evan W. McConnell Leslie M. Hicks Leslie B. Poole Robert H. Newman Dukka B. KC
author_facet	Hussam J. AL-barakati Evan W. McConnell Leslie M. Hicks Leslie B. Poole Robert H. Newman Dukka B. KC
author_sort	Hussam J. AL-barakati
title	SVM-SulfoSite: A support vector machine based predictor for sulfenylation sites
title_short	SVM-SulfoSite: A support vector machine based predictor for sulfenylation sites
title_full	SVM-SulfoSite: A support vector machine based predictor for sulfenylation sites
title_fullStr	SVM-SulfoSite: A support vector machine based predictor for sulfenylation sites
title_full_unstemmed	SVM-SulfoSite: A support vector machine based predictor for sulfenylation sites
title_sort	svm-sulfosite: a support vector machine based predictor for sulfenylation sites
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/a2f299fb10184e2fa23fde2539f4dae7
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SVM-SulfoSite: A support vector machine based predictor for sulfenylation sites

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