{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T01:59:15Z","timestamp":1762999155903,"version":"3.41.0"},"reference-count":54,"publisher":"Springer Science and Business Media LLC","issue":"S18","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/1471-2105-16-s18-s10","type":"journal-article","created":{"date-parts":[[2015,12,10]],"date-time":"2015-12-10T05:02:21Z","timestamp":1449723741000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":41,"title":["A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs"],"prefix":"10.1186","volume":"16","author":[{"given":"Hui-Ju","family":"Kao","sequence":"first","affiliation":[]},{"given":"Chien-Hsun","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Neil Arvin","family":"Breta\u00f1a","sequence":"additional","affiliation":[]},{"given":"Cheng-Tsung","family":"Lu","sequence":"additional","affiliation":[]},{"given":"Kai-Yao","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Shun-Long","family":"Weng","sequence":"additional","affiliation":[]},{"given":"Tzong-Yi","family":"Lee","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,12,9]]},"reference":[{"issue":"7139","key":"7201_CR1","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1038\/nature05815","volume":"446","author":"GW Hart","year":"2007","unstructured":"Hart GW, Housley MP, Slawson C: Cycling of O-linked beta-N-acetylglucosamine on nucleocytoplasmic proteins. Nature. 2007, 446 (7139): 1017-1022.","journal-title":"Nature"},{"issue":"1","key":"7201_CR2","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/S0304-4165(99)00176-2","volume":"1473","author":"FI Comer","year":"1999","unstructured":"Comer FI, Hart GW: O-GlcNAc and the control of gene expression. Biochim Biophys Acta. 1999, 1473 (1): 161-171.","journal-title":"Biochim Biophys Acta"},{"issue":"2","key":"7201_CR3","doi-asserted-by":"crossref","first-page":"224","DOI":"10.4331\/wjbc.v5.i2.224","volume":"5","author":"M Ogawa","year":"2014","unstructured":"Ogawa M, Furukawa K, Okajima T: Extracellular O-linked beta-N-acetylglucosamine: Its biology and relationship to human disease. World J Biol Chem. 2014, 5 (2): 224-230.","journal-title":"World J Biol Chem"},{"key":"7201_CR4","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/ncomms1591","volume":"2","author":"Y Sakaidani","year":"2011","unstructured":"Sakaidani Y, Nomura T, Matsuura A, Ito M, Suzuki E, Murakami K, Nadano D, Matsuda T, Furukawa K, Okajima T: O-linked-N-acetylglucosamine on extracellular protein domains mediates epithelial cell-matrix interactions. Nat Commun. 2011, 2: 583-","journal-title":"Nat Commun"},{"key":"7201_CR5","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1016\/j.plaphy.2014.07.021","volume":"83","author":"A Delporte","year":"2014","unstructured":"Delporte A, De Zaeytijd J, De Storme N, Azmi A, Geelen D, Smagghe G, Guisez Y, Van Damme EJ: Cell cycle-dependent O-GlcNAc modification of tobacco histones and their interaction with the tobacco lectin. Plant Physiol Biochem. 2014, 83: 151-158.","journal-title":"Plant Physiol Biochem"},{"key":"7201_CR6","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1007\/978-1-4939-0992-6_7","volume":"1176","author":"CM Ferrer","year":"2014","unstructured":"Ferrer CM, Reginato MJ: Cancer metabolism: cross talk between signaling and O-GlcNAcylation. Methods Mol Biol. 2014, 1176: 73-88.","journal-title":"Methods Mol Biol"},{"key":"7201_CR7","first-page":"145","volume":"5","author":"P Jozwiak","year":"2014","unstructured":"Jozwiak P, Forma E, Brys M, Krzeslak A: O-GlcNAcylation and Metabolic Reprograming in Cancer. Front Endocrinol (Lausanne). 2014, 5: 145-","journal-title":"Front Endocrinol (Lausanne)"},{"issue":"8","key":"7201_CR8","doi-asserted-by":"publisher","first-page":"1003","DOI":"10.2337\/diab.45.8.1003","volume":"45","author":"DA McClain","year":"1996","unstructured":"McClain DA, Crook ED: Hexosamines and insulin resistance. Diabetes. 1996, 45 (8): 1003-1009.","journal-title":"Diabetes"},{"issue":"29","key":"7201_CR9","doi-asserted-by":"publisher","first-page":"10804","DOI":"10.1073\/pnas.0400348101","volume":"101","author":"F Liu","year":"2004","unstructured":"Liu F, Iqbal K, Grundke-Iqbal I, Hart GW, Gong CX: O-GlcNAcylation regulates phosphorylation of tau: a mechanism involved in Alzheimer's disease. Proc Natl Acad Sci USA. 2004, 101 (29): 10804-10809.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"4","key":"7201_CR10","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1016\/j.bbadis.2011.01.009","volume":"1812","author":"W Mi","year":"2011","unstructured":"Mi W, Gu Y, Han C, Liu H, Fan Q, Zhang X, Cong Q, Yu W: O-GlcNAcylation is a novel regulator of lung and colon cancer malignancy. Biochim Biophys Acta. 2011, 1812 (4): 514-519.","journal-title":"Biochim Biophys Acta"},{"key":"7201_CR11","doi-asserted-by":"crossref","first-page":"99","DOI":"10.3389\/fendo.2013.00099","volume":"4","author":"Y Fardini","year":"2013","unstructured":"Fardini Y, Dehennaut V, Lefebvre T, Issad T: O-GlcNAcylation: A New Cancer Hallmark?. Front Endocrinol (Lausanne). 2013, 4: 99-","journal-title":"Front Endocrinol (Lausanne)"},{"issue":"51","key":"7201_CR12","doi-asserted-by":"publisher","first-page":"36418","DOI":"10.1074\/jbc.M113.495713","volume":"288","author":"X Huang","year":"2013","unstructured":"Huang X, Pan Q, Sun D, Chen W, Shen A, Huang M, Ding J, Geng M: O-GlcNAcylation of cofilin promotes breast cancer cell invasion. J Biol Chem. 2013, 288 (51): 36418-36425.","journal-title":"J Biol Chem"},{"issue":"5","key":"7201_CR13","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1074\/mcp.T500040-MCP200","volume":"5","author":"K Vosseller","year":"2006","unstructured":"Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor JO, Guan S, Medzihradszky KF, Maltby DA, et al: O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry. Mol Cell Proteomics. 2006, 5 (5): 923-934.","journal-title":"Mol Cell Proteomics"},{"issue":"8","key":"7201_CR14","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1074\/mcp.O112.018366","volume":"11","author":"JC Trinidad","year":"2012","unstructured":"Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL: Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse. Mol Cell Proteomics. 2012, 11 (8): 215-229.","journal-title":"Mol Cell Proteomics"},{"issue":"19","key":"7201_CR15","doi-asserted-by":"publisher","first-page":"7280","DOI":"10.1073\/pnas.1200425109","volume":"109","author":"JF Alfaro","year":"2012","unstructured":"Alfaro JF, Gong CX, Monroe ME, Aldrich JT, Clauss TR, Purvine SO, Wang Z, Camp DG, Shabanowitz J, Stanley P, et al: Tandem mass spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets. Proc Natl Acad Sci USA. 2012, 109 (19): 7280-7285.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"6","key":"7201_CR16","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1038\/nchembio881","volume":"3","author":"N Khidekel","year":"2007","unstructured":"Khidekel N, Ficarro SB, Clark PM, Bryan MC, Swaney DL, Rexach JE, Sun YE, Coon JJ, Peters EC, Hsieh-Wilson LC: Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics. Nat Chem Biol. 2007, 3 (6): 339-348.","journal-title":"Nat Chem Biol"},{"issue":"23","key":"7201_CR17","doi-asserted-by":"publisher","first-page":"9490","DOI":"10.1073\/pnas.1019289108","volume":"108","author":"SA Myers","year":"2011","unstructured":"Myers SA, Panning B, Burlingame AL: Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells. Proc Natl Acad Sci USA. 2011, 108 (23): 9490-9495.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"2","key":"7201_CR18","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1021\/ac051207j","volume":"78","author":"A Nandi","year":"2006","unstructured":"Nandi A, Sprung R, Barma DK, Zhao Y, Kim SC, Falck JR: Global identification of O-GlcNAc-modified proteins. Anal Chem. 2006, 78 (2): 452-458.","journal-title":"Anal Chem"},{"issue":"1","key":"7201_CR19","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1074\/mcp.M900268-MCP200","volume":"9","author":"Z Wang","year":"2010","unstructured":"Wang Z, Udeshi ND, O'Malley M, Shabanowitz J, Hunt DF, Hart GW: Enrichment and site mapping of O-linked N-acetylglucosamine by a combination of chemical\/enzymatic tagging, photochemical cleavage, and electron transfer dissociation mass spectrometry. Mol Cell Proteomics. 2010, 9 (1): 153-160.","journal-title":"Mol Cell Proteomics"},{"key":"7201_CR20","first-page":"310","volume-title":"Pac Symp Biocomput","author":"R Gupta","year":"2002","unstructured":"Gupta R, Brunak S: Prediction of glycosylation across the human proteome and the correlation to protein function. Pac Symp Biocomput. 2002, 310-322."},{"key":"7201_CR21","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1186\/1471-2105-11-536","volume":"11","author":"SA Chen","year":"2010","unstructured":"Chen SA, Lee TY, Ou YY: Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins. BMC Bioinformatics. 2010, 11: 536-","journal-title":"BMC Bioinformatics"},{"key":"7201_CR22","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1186\/1471-2105-12-91","volume":"12","author":"J Wang","year":"2011","unstructured":"Wang J, Torii M, Liu H, Hart GW, Hu ZZ: dbOGAP - an integrated bioinformatics resource for protein O-GlcNAcylation. BMC Bioinformatics. 2011, 12: 91-","journal-title":"BMC Bioinformatics"},{"issue":"11","key":"7201_CR23","doi-asserted-by":"publisher","first-page":"2909","DOI":"10.1039\/c3mb70326f","volume":"9","author":"CZ Jia","year":"2013","unstructured":"Jia CZ, Liu T, Wang ZP: O-GlcNAcPRED: a sensitive predictor to capture protein O-GlcNAcylation sites. Mol Biosyst. 2013, 9 (11): 2909-2913.","journal-title":"Mol Biosyst"},{"key":"7201_CR24","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1186\/1471-2105-8-438","volume":"8","author":"C Caragea","year":"2007","unstructured":"Caragea C, Sinapov J, Silvescu A, Dobbs D, Honavar V: Glycosylation site prediction using ensembles of Support Vector Machine classifiers. BMC Bioinformatics. 2007, 8: 438-","journal-title":"BMC Bioinformatics"},{"issue":"5-6","key":"7201_CR25","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1016\/j.cbpa.2012.10.021","volume":"16","author":"DJ Vocadlo","year":"2012","unstructured":"Vocadlo DJ: O-GlcNAc processing enzymes: catalytic mechanisms, substrate specificity, and enzyme regulation. Curr Opin Chem Biol. 2012, 16 (5-6): 488-497.","journal-title":"Curr Opin Chem Biol"},{"issue":"Suppl 16","key":"7201_CR26","doi-asserted-by":"publisher","first-page":"S1","DOI":"10.1186\/1471-2105-15-S16-S1","volume":"15","author":"HY Wu","year":"2014","unstructured":"Wu HY, Lu CT, Kao HJ, Chen YJ, Chen YJ, Lee TY: Characterization and identification of protein O-GlcNAcylation sites with substrate specificity. BMC bioinformatics. 2014, 15 (Suppl 16): S1-","journal-title":"BMC bioinformatics"},{"issue":"1-2","key":"7201_CR27","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1016\/j.jchromb.2006.09.041","volume":"849","author":"M Wuhrer","year":"2007","unstructured":"Wuhrer M, Catalina MI, Deelder AM, Hokke CH: Glycoproteomics based on tandem mass spectrometry of glycopeptides. J Chromatogr B Analyt Technol Biomed Life Sci. 2007, 849 (1-2): 115-128.","journal-title":"J Chromatogr B Analyt Technol Biomed Life Sci"},{"issue":"Database","key":"7201_CR28","doi-asserted-by":"publisher","first-page":"D622","DOI":"10.1093\/nar\/gkj083","volume":"34","author":"TY Lee","year":"2006","unstructured":"Lee TY, Huang HD, Hung JH, Huang HY, Yang YS, Wang TH: dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res. 2006, 34 (Database): D622-627.","journal-title":"Nucleic Acids Res"},{"issue":"Database","key":"7201_CR29","doi-asserted-by":"publisher","first-page":"D295","DOI":"10.1093\/nar\/gks1229","volume":"41","author":"CT Lu","year":"2013","unstructured":"Lu CT, Huang KY, Su MG, Lee TY, Bretana NA, Chang WC, Chen YJ, Huang HD: DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. Nucleic Acids Res. 2013, 41 (Database): D295-305.","journal-title":"Nucleic Acids Res"},{"issue":"Database","key":"7201_CR30","doi-asserted-by":"publisher","first-page":"D537","DOI":"10.1093\/nar\/gkt1221","volume":"42","author":"MG Su","year":"2014","unstructured":"Su MG, Huang KY, Lu CT, Kao HJ, Chang YH, Lee TY: topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins. Nucleic Acids Res. 2014, 42 (Database): D537-545.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"7201_CR31","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1093\/nar\/27.1.370","volume":"27","author":"R Gupta","year":"1999","unstructured":"Gupta R, Birch H, Rapacki K, Brunak S, Hansen JE: O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins. Nucleic Acids Res. 1999, 27 (1): 370-372.","journal-title":"Nucleic Acids Res"},{"issue":"Database","key":"7201_CR32","doi-asserted-by":"publisher","first-page":"D115","DOI":"10.1093\/nar\/gkh131","volume":"32","author":"R Apweiler","year":"2004","unstructured":"Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, et al: UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 2004, 32 (Database): D115-119.","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"7201_CR33","doi-asserted-by":"publisher","first-page":"1032","DOI":"10.1002\/jcc.20235","volume":"26","author":"HD Huang","year":"2005","unstructured":"Huang HD, Lee TY, Tzeng SW, Wu LC, Horng JT, Tsou AP, Huang KT: Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites. J Comput Chem. 2005, 26 (10): 1032-1041.","journal-title":"J Comput Chem"},{"issue":"Web Server","key":"7201_CR34","doi-asserted-by":"publisher","first-page":"W226","DOI":"10.1093\/nar\/gki471","volume":"33","author":"HD Huang","year":"2005","unstructured":"Huang HD, Lee TY, Tzeng SW, Horng JT: KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res. 2005, 33 (Web Server): W226-229.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"7201_CR35","doi-asserted-by":"publisher","first-page":"e63452","DOI":"10.1371\/journal.pone.0063452","volume":"8","author":"X Ma","year":"2013","unstructured":"Ma X, Liu P, Yan H, Sun H, Liu X, Zhou F, Li L, Chen Y, Muthana MM, Chen \u00d7, et al: Substrate specificity provides insights into the sugar donor recognition mechanism of O-GlcNAc transferase (OGT). PLoS One. 2013, 8 (5): e63452-","journal-title":"PLoS One"},{"issue":"13","key":"7201_CR36","doi-asserted-by":"publisher","first-page":"1780","DOI":"10.1093\/bioinformatics\/btr291","volume":"27","author":"TY Lee","year":"2011","unstructured":"Lee TY, Lin ZQ, Hsieh SJ, Bretana NA, Lu CT: Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences. Bioinformatics. 2011, 27 (13): 1780-1787.","journal-title":"Bioinformatics"},{"issue":"Suppl 1","key":"7201_CR37","doi-asserted-by":"publisher","first-page":"S1","DOI":"10.1186\/1471-2105-16-S1-S1","volume":"16","author":"VN Nguyen","year":"2015","unstructured":"Nguyen VN, Huang KY, Huang CH, Chang TH, Bretana N, Lai K, Weng J, Lee TY: Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities. BMC bioinformatics. 2015, 16 (Suppl 1): S1-","journal-title":"BMC bioinformatics"},{"issue":"1","key":"7201_CR38","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","volume":"268","author":"C Burge","year":"1997","unstructured":"Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997, 268 (1): 78-94.","journal-title":"J Mol Biol"},{"issue":"9","key":"7201_CR39","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","volume":"14","author":"SR Eddy","year":"1998","unstructured":"Eddy SR: Profile hidden Markov models. Bioinformatics. 1998, 14 (9): 755-763.","journal-title":"Bioinformatics"},{"issue":"27","key":"7201_CR40","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1145\/1961189.1961199","volume":"2","author":"CC Chang","year":"2011","unstructured":"Chang CC, Lin CJ: LIBSVM : a library for support vector machines. ACM Transactions on Intelligent Systems and Technology. 2011, 2 (27): 1-27.","journal-title":"ACM Transactions on Intelligent Systems and Technology"},{"issue":"9","key":"7201_CR41","doi-asserted-by":"publisher","first-page":"1532","DOI":"10.1002\/jcc.21232","volume":"30","author":"DM Shien","year":"2009","unstructured":"Shien DM, Lee TY, Chang WC, Hsu JB, Horng JT, Hsu PC, Wang TY, Huang HD: Incorporating structural characteristics for identification of protein methylation sites. J Comput Chem. 2009, 30 (9): 1532-1543.","journal-title":"J Comput Chem"},{"key":"7201_CR42","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1186\/1471-2105-12-261","volume":"12","author":"TY Lee","year":"2011","unstructured":"Lee TY, Bretana NA, Lu CT: PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity. BMC Bioinformatics. 2011, 12: 261-","journal-title":"BMC Bioinformatics"},{"issue":"Database","key":"7201_CR43","doi-asserted-by":"publisher","first-page":"D777","DOI":"10.1093\/nar\/gkq970","volume":"39","author":"TY Lee","year":"2011","unstructured":"Lee TY, Bo-Kai Hsu J, Chang WC, Huang HD: RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. Nucleic Acids Res. 2011, 39 (Database): D777-787.","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"7201_CR44","doi-asserted-by":"publisher","first-page":"1598","DOI":"10.1074\/mcp.M700574-MCP200","volume":"7","author":"Y Xue","year":"2008","unstructured":"Xue Y, Ren J, Gao X, Jin C, Wen L, Yao X: GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol Cell Proteomics. 2008, 7 (9): 1598-1608.","journal-title":"Mol Cell Proteomics"},{"issue":"Web Server","key":"7201_CR45","doi-asserted-by":"publisher","first-page":"W588","DOI":"10.1093\/nar\/gkm322","volume":"35","author":"YH Wong","year":"2007","unstructured":"Wong YH, Lee TY, Liang HK, Huang CM, Wang TY, Yang YH, Chu CH, Huang HD, Ko MT, Hwang JK: KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res. 2007, 35 (Web Server): W588-594.","journal-title":"Nucleic Acids Res"},{"key":"7201_CR46","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1186\/1471-2105-7-163","volume":"7","author":"Y Xue","year":"2006","unstructured":"Xue Y, Li A, Wang L, Feng H, Yao X: PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory. BMC Bioinformatics. 2006, 7: 163-","journal-title":"BMC Bioinformatics"},{"key":"7201_CR47","doi-asserted-by":"publisher","first-page":"bau034","DOI":"10.1093\/database\/bau034","volume":"2014","author":"KY Huang","year":"2014","unstructured":"Huang KY, Wu HY, Chen YJ, Lu CT, Su MG, Hsieh YC, Tsai CM, Lin KI, Huang HD, Lee TY, et al: RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. Database : the journal of biological databases and curation. 2014, 2014: bau034-","journal-title":"Database : the journal of biological databases and curation"},{"issue":"10","key":"7201_CR48","doi-asserted-by":"publisher","first-page":"987","DOI":"10.1007\/s10822-011-9477-2","volume":"25","author":"CT Lu","year":"2011","unstructured":"Lu CT, Chen SA, Bretana NA, Cheng TH, Lee TY: Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites. J Comput Aided Mol Des. 2011, 25 (10): 987-995.","journal-title":"J Comput Aided Mol Des"},{"issue":"Database","key":"7201_CR49","doi-asserted-by":"publisher","first-page":"D261","DOI":"10.1093\/nar\/gkr1122","volume":"40","author":"PV Hornbeck","year":"2012","unstructured":"Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M: PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 2012, 40 (Database): D261-270.","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"7201_CR50","doi-asserted-by":"publisher","first-page":"1536","DOI":"10.1093\/bioinformatics\/btl151","volume":"22","author":"V Vacic","year":"2006","unstructured":"Vacic V, Iakoucheva LM, Radivojac P: Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics. 2006, 22 (12): 1536-1537.","journal-title":"Bioinformatics"},{"issue":"1","key":"7201_CR51","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1002\/prot.21677","volume":"71","author":"M Kumar","year":"2008","unstructured":"Kumar M, Gromiha MM, Raghava GP: Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins. 2008, 71 (1): 189-194.","journal-title":"Proteins"},{"issue":"Suppl 16","key":"7201_CR52","doi-asserted-by":"publisher","first-page":"S10","DOI":"10.1186\/1471-2105-14-S16-S10","volume":"14","author":"KY Huang","year":"2013","unstructured":"Huang KY, Lu CT, Bretana N, Lee TY, Chang TH: ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins. BMC Bioinformatics. 2013, 14 (Suppl 16): S10-","journal-title":"BMC Bioinformatics"},{"issue":"32","key":"7201_CR53","doi-asserted-by":"publisher","first-page":"21327","DOI":"10.1074\/jbc.M109.007310","volume":"284","author":"WB Dias","year":"2009","unstructured":"Dias WB, Cheung WD, Wang Z, Hart GW: Regulation of calcium\/calmodulin-dependent kinase IV by O-GlcNAc modification. J Biol Chem. 2009, 284 (32): 21327-21337.","journal-title":"J Biol Chem"},{"issue":"Suppl 16","key":"7201_CR54","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1471-2105-14-S16-S2","volume":"14","author":"MG Su","year":"2013","unstructured":"Su MG, Lee TY: Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures. BMC Bioinformatics. 2013, 14 (Suppl 16): S2-","journal-title":"BMC Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-16-S18-S10.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,31]],"date-time":"2025-05-31T18:46:24Z","timestamp":1748717184000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-16-S18-S10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,12]]},"references-count":54,"journal-issue":{"issue":"S18","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["7201"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-16-s18-s10","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2015,12]]},"assertion":[{"value":"9 December 2015","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S10"}}