{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:54:24Z","timestamp":1767963264614,"version":"3.49.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>S-sulfenylation (S-sulphenylation, or sulfenic acid), the covalent attachment of S-hydroxyl (\u2013SOH) to cysteine thiol, plays a significant role in redox regulation of protein functions. Although sulfenic acid is transient and labile, most of its physiological activities occur under control of S-hydroxylation. Therefore, discriminating the substrate site of S-sulfenylated proteins is an essential task in computational biology for the furtherance of protein structures and functions. Research into S-sulfenylated protein is currently very limited, and no dedicated tools are available for the computational identification of SOH sites. Given a total of 1096 experimentally verified S-sulfenylated proteins from humans, this study carries out a bioinformatics investigation on SOH sites based on amino acid composition and solvent-accessible surface area. A TwoSampleLogo indicates that the positively and negatively charged amino acids flanking the SOH sites may impact the formulation of S-sulfenylation in closed three-dimensional environments. In addition, the substrate motifs of SOH sites are studied using the maximal dependence decomposition (MDD). Based on the concept of binary classification between SOH and non-SOH sites, Support vector machine (SVM) is applied to learn the predictive model from MDD-identified substrate motifs. According to the evaluation results of 5-fold cross-validation, the integrated SVM model learned from substrate motifs yields an average accuracy of 0.87, significantly improving the prediction of SOH sites. Furthermore, the integrated SVM model also effectively improves the predictive performance in an independent testing set. Finally, the integrated SVM model is applied to implement an effective web resource, named MDD-SOH, to identify SOH sites with their corresponding substrate motifs.<\/jats:p>\n               <jats:p>Availability and implementation: The MDD-SOH is now freely available to all interested users at http:\/\/csb.cse.yzu.edu.tw\/MDDSOH\/. All of the data set used in this work is also available for download in the website.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <jats:p>Contact: \u00a0francis@saturn.yzu.edu.tw<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv558","type":"journal-article","created":{"date-parts":[[2015,9,27]],"date-time":"2015-09-27T23:57:20Z","timestamp":1443398240000},"page":"165-172","source":"Crossref","is-referenced-by-count":30,"title":["MDD\u2013SOH: exploiting maximal dependence decomposition to identify <i>S<\/i>-sulfenylation sites with substrate motifs"],"prefix":"10.1093","volume":"32","author":[{"given":"Van-Minh","family":"Bui","sequence":"first","affiliation":[{"name":"1 Department of Computer Science and Engineering and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng-Tsung","family":"Lu","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thi-Trang","family":"Ho","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tzong-Yi","family":"Lee","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering and"},{"name":"2 Innovation Center for Big Data and Digital Convergence, Yuan Ze University, Taoyuan 320, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,9,26]]},"reference":[{"key":"2023020110255977500_btv558-B1","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1002\/prot.10328","article-title":"Real value prediction of solvent accessibility from amino acid sequence","volume":"50","author":"Ahmad","year":"2003","journal-title":"Proteins"},{"key":"2023020110255977500_btv558-B2","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1093\/bioinformatics\/btg249","article-title":"RVP-net: online prediction of real valued accessible surface area of proteins from single sequences","volume":"19","author":"Ahmad","year":"2003","journal-title":"Bioinformatics"},{"key":"2023020110255977500_btv558-B3","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023020110255977500_btv558-B4","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023020110255977500_btv558-B5","doi-asserted-by":"crossref","first-page":"e40694","DOI":"10.1371\/journal.pone.0040694","article-title":"Identifying protein phosphorylation sites with kinase substrate specificity on human viruses","volume":"7","author":"Bretana","year":"2012","journal-title":"PLoS One"},{"key":"2023020110255977500_btv558-B6","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","article-title":"Prediction of complete gene structures in human genomic DNA","volume":"268","author":"Burge","year":"1997","journal-title":"J. Mol. Biol."},{"key":"2023020110255977500_btv558-B7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/1961189.1961199","article-title":"LIBSVM : a library for support vector machines","volume":"2","author":"Chang","year":"2011","journal-title":"ACM Trans. Intel. Syst. Technol."},{"key":"2023020110255977500_btv558-B8","doi-asserted-by":"crossref","first-page":"2526","DOI":"10.1002\/jcc.21258","article-title":"Incorporating support vector machine for identifying protein tyrosine sulfation sites","volume":"30","author":"Chang","year":"2009","journal-title":"J. Comput. 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Chem."},{"key":"2023020110255977500_btv558-B15","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1186\/1471-2105-12-261","article-title":"PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity","volume":"12","author":"Lee","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023020110255977500_btv558-B16","doi-asserted-by":"crossref","first-page":"2293","DOI":"10.1093\/bioinformatics\/bts436","article-title":"dbSNO: a database of cysteine S-nitrosylation","volume":"28","author":"Lee","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020110255977500_btv558-B17","doi-asserted-by":"crossref","first-page":"e21849","DOI":"10.1371\/journal.pone.0021849","article-title":"SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity","volume":"6","author":"Lee","year":"2011","journal-title":"PLoS One"},{"key":"2023020110255977500_btv558-B18","doi-asserted-by":"crossref","first-page":"1780","DOI":"10.1093\/bioinformatics\/btr291","article-title":"Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences","volume":"27","author":"Lee","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020110255977500_btv558-B19","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.cbpa.2010.11.012","article-title":"Chemical \u2018omics\u2019 approaches for understanding protein cysteine oxidation in biology","volume":"15","author":"Leonard","year":"2011","journal-title":"Curr. Opin. Chem. Biol."},{"key":"2023020110255977500_btv558-B20","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020110255977500_btv558-B21","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1007\/s10822-011-9477-2","article-title":"Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites","volume":"25","author":"Lu","year":"2011","journal-title":"J. Comput. Aided Mol. Des."},{"key":"2023020110255977500_btv558-B22","doi-asserted-by":"crossref","first-page":"4419","DOI":"10.1074\/jbc.R111.275578","article-title":"Analysis and functional prediction of reactive cysteine residues","volume":"287","author":"Marino","year":"2012","journal-title":"J. Biol. Chem."},{"key":"2023020110255977500_btv558-B23","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/0005-2795(75)90109-9","article-title":"Comparison of the predicted and observed secondary structure of T4 phage lysozyme","volume":"405","author":"Matthews","year":"1975","journal-title":"Biochim. Biophys. Acta"},{"key":"2023020110255977500_btv558-B24","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1002\/prot.10047","article-title":"Predicting the disulfide bonding state of cysteines using protein descriptors","volume":"46","author":"Mucchielli-Giorgi","year":"2002","journal-title":"Proteins"},{"key":"2023020110255977500_btv558-B25","doi-asserted-by":"crossref","first-page":"1833","DOI":"10.1021\/pr060674u","article-title":"Surface accessibility of protein post-translational modifications","volume":"6","author":"Pang","year":"2007","journal-title":"J. Proteome Res."},{"key":"2023020110255977500_btv558-B26","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.cbpa.2008.01.021","article-title":"Discovering mechanisms of signaling-mediated cysteine oxidation","volume":"12","author":"Poole","year":"2008","journal-title":"Curr. Opin. Chem. Biol."},{"key":"2023020110255977500_btv558-B27","doi-asserted-by":"crossref","first-page":"1410","DOI":"10.1002\/cbic.201300396","article-title":"An isotopically tagged azobenzene-based cleavable linker for quantitative proteomics","volume":"14","author":"Qian","year":"2013","journal-title":"ChemBioChem."},{"key":"2023020110255977500_btv558-B28","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/j.freeradbiomed.2011.04.031","article-title":"Protein sulfenic acid formation: from cellular damage to redox regulation","volume":"51","author":"Roos","year":"2011","journal-title":"Free Radic. Biol. Med."},{"key":"2023020110255977500_btv558-B29","doi-asserted-by":"crossref","first-page":"1342","DOI":"10.1002\/anie.201007175","article-title":"Quantification of protein sulfenic acid modifications using isotope-coded dimedone and iododimedone","volume":"50","author":"Seo","year":"2011","journal-title":"Angew. Chem.-Int. Edit."},{"key":"2023020110255977500_btv558-B30","doi-asserted-by":"crossref","first-page":"2551","DOI":"10.1093\/bioinformatics\/bts468","article-title":"RedoxDB\u2014a curated database for experimentally verified protein oxidative modification","volume":"28","author":"Sun","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020110255977500_btv558-B31","doi-asserted-by":"crossref","first-page":"18351","DOI":"10.1021\/ja1083909","article-title":"Cleavable biotin probes for labeling of biomolecules via the azide \u2013 alkyne cycloaddition","volume":"132","author":"Szychowski","year":"2010","journal-title":"J. Am. Chem. Soc."},{"key":"2023020110255977500_btv558-B32","doi-asserted-by":"crossref","first-page":"1536","DOI":"10.1093\/bioinformatics\/btl151","article-title":"Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments","volume":"22","author":"Vacic","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020110255977500_btv558-B33","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1038\/nmeth.2759","article-title":"A chemoproteomic platform to quantitatively map targets of lipid-derived electrophiles","volume":"11","author":"Wang","year":"2014","journal-title":"Nat. Methods"},{"key":"2023020110255977500_btv558-B34","doi-asserted-by":"crossref","first-page":"10550","DOI":"10.1073\/pnas.1011665108","article-title":"Isoform-specific regulation of Akt by PDGF-induced reactive oxygen species, Proc","volume":"108","author":"Wani","year":"2011","journal-title":"Natl. Acad. Sci."},{"key":"2023020110255977500_btv558-B35","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1038\/nature09472","article-title":"Quantitative reactivity profiling predicts functional cysteines in proteomes","volume":"468","author":"Weerapana","year":"2010","journal-title":"Nature"},{"key":"2023020110255977500_btv558-B36","doi-asserted-by":"crossref","first-page":"W588","DOI":"10.1093\/nar\/gkm322","article-title":"KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns","volume":"35","author":"Wong","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023020110255977500_btv558-B37","doi-asserted-by":"crossref","first-page":"4776","DOI":"10.1038\/ncomms5776","article-title":"Site-specific mapping and quantification of protein S-sulphenylation in cells","volume":"5","author":"Yang","year":"2014","journal-title":"Nat. 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