{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:24:17Z","timestamp":1767961457080,"version":"3.49.0"},"reference-count":58,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2009,4,21]],"date-time":"2009-04-21T00:00:00Z","timestamp":1240272000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,12]]},"DOI":"10.1186\/1471-2105-10-117","type":"journal-article","created":{"date-parts":[[2009,4,21]],"date-time":"2009-04-21T14:13:58Z","timestamp":1240323238000},"source":"Crossref","is-referenced-by-count":65,"title":["Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins"],"prefix":"10.1186","volume":"10","author":[{"given":"Pawel","family":"Durek","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Schudoma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wolfram","family":"Weckwerth","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joachim","family":"Selbig","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dirk","family":"Walther","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,4,21]]},"reference":[{"issue":"Pt 3","key":"2847_CR1","doi-asserted-by":"publisher","first-page":"729","DOI":"10.1042\/bj3180729","volume":"318","author":"DT Denhardt","year":"1996","unstructured":"Denhardt DT: Signal-transducing protein phosphorylation cascades mediated by Ras\/Rho proteins in the mammalian cell: the potential for multiplex signalling. Biochem J 1996, 318(Pt 3):729\u2013747.","journal-title":"Biochem J"},{"issue":"6757","key":"2847_CR2","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1038\/46925","volume":"402","author":"MB Yaffe","year":"1999","unstructured":"Yaffe MB, Cantley LC: Signal transduction. Grabbing phosphoproteins. Nature 1999, 402(6757):30\u201331. 10.1038\/46925","journal-title":"Nature"},{"issue":"4","key":"2847_CR3","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1016\/0968-0004(93)90019-J","volume":"18","author":"E Nishida","year":"1993","unstructured":"Nishida E, Gotoh Y: The MAP kinase cascade is essential for diverse signal transduction pathways. Trends Biochem Sci 1993, 18(4):128\u2013131. 10.1016\/0968-0004(93)90019-J","journal-title":"Trends Biochem Sci"},{"key":"2847_CR4","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1146\/annurev.bb.22.060193.001215","volume":"22","author":"LN Johnson","year":"1993","unstructured":"Johnson LN, Barford D: The effects of phosphorylation on the structure and function of proteins. Annu Rev Biophys Biomol Struct 1993, 22: 199\u2013232. 10.1146\/annurev.bb.22.060193.001215","journal-title":"Annu Rev Biophys Biomol Struct"},{"issue":"13","key":"2847_CR5","doi-asserted-by":"publisher","first-page":"3635","DOI":"10.1093\/nar\/gkg584","volume":"31","author":"JC Obenauer","year":"2003","unstructured":"Obenauer JC, Cantley LC, Yaffe MB: Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 2003, 31(13):3635\u20133641. 10.1093\/nar\/gkg584","journal-title":"Nucleic Acids Res"},{"key":"2847_CR6","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. 10.1186\/1471-2105-7-163","journal-title":"BMC Bioinformatics"},{"issue":"17","key":"2847_CR7","doi-asserted-by":"publisher","first-page":"3179","DOI":"10.1093\/bioinformatics\/bth382","volume":"20","author":"JH Kim","year":"2004","unstructured":"Kim JH, Lee J, Oh B, Kimm K, Koh I: Prediction of phosphorylation sites using SVMs. Bioinformatics 2004, 20(17):3179\u20133184. 10.1093\/bioinformatics\/bth382","journal-title":"Bioinformatics"},{"issue":"1","key":"2847_CR8","first-page":"73","volume":"10","author":"D Plewczynski","year":"2005","unstructured":"Plewczynski D, Tkacz A, Godzik A, Rychlewski L: A support vector machine approach to the identification of phosphorylation sites. Cell Mol Biol Lett 2005, 10(1):73\u201389.","journal-title":"Cell Mol Biol Lett"},{"issue":"6","key":"2847_CR9","doi-asserted-by":"publisher","first-page":"1633","DOI":"10.1002\/pmic.200300771","volume":"4","author":"N Blom","year":"2004","unstructured":"Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S: Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 2004, 4(6):1633\u20131649. 10.1002\/pmic.200300771","journal-title":"Proteomics"},{"issue":"3","key":"2847_CR10","doi-asserted-by":"publisher","first-page":"1037","DOI":"10.1093\/nar\/gkh253","volume":"32","author":"LM Iakoucheva","year":"2004","unstructured":"Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, Obradovic Z, Dunker AK: The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res 2004, 32(3):1037\u20131049. 10.1093\/nar\/gkh253","journal-title":"Nucleic Acids Res"},{"key":"2847_CR11","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1186\/1471-2105-5-79","volume":"5","author":"F Diella","year":"2004","unstructured":"Diella F, Cameron S, Gemund C, Linding R, Via A, Kuster B, Sicheritz-Ponten T, Blom N, Gibson TJ: Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics 2004, 5: 79. 10.1186\/1471-2105-5-79","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"2847_CR12","doi-asserted-by":"publisher","first-page":"R90","DOI":"10.1186\/gb-2007-8-5-r90","volume":"8","author":"JL Jimenez","year":"2007","unstructured":"Jimenez JL, Hegemann B, Hutchins JR, Peters JM, Durbin R: A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database. Genome Biol 2007, 8(5):R90. 10.1186\/gb-2007-8-5-r90","journal-title":"Genome Biol"},{"issue":"4","key":"2847_CR13","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/S1672-0229(05)03029-9","volume":"3","author":"SC Fan","year":"2005","unstructured":"Fan SC, Zhang XG: Characterizing the microenvironment surrounding phosphorylated protein sites. Genomics Proteomics Bioinformatics 2005, 3(4):213\u2013217.","journal-title":"Genomics Proteomics Bioinformatics"},{"issue":"9","key":"2847_CR14","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1016\/0968-0004(90)90073-K","volume":"15","author":"BE Kemp","year":"1990","unstructured":"Kemp BE, Pearson RB: Protein kinase recognition sequence motifs. Trends Biochem Sci 1990, 15(9):342\u2013346. 10.1016\/0968-0004(90)90073-K","journal-title":"Trends Biochem Sci"},{"issue":"3","key":"2847_CR15","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/S0167-4889(96)00083-3","volume":"1314","author":"LA Pinna","year":"1996","unstructured":"Pinna LA, Ruzzene M: How do protein kinases recognize their substrates? Biochimica et Biophysica Acta (BBA) \u2013 Molecular Cell Research 1996, 1314(3):191\u2013225. 10.1016\/S0167-4889(96)00083-3","journal-title":"Biochimica et Biophysica Acta (BBA) \u2013 Molecular Cell Research"},{"issue":"5","key":"2847_CR16","doi-asserted-by":"publisher","first-page":"1351","DOI":"10.1006\/jmbi.1999.3310","volume":"294","author":"N Blom","year":"1999","unstructured":"Blom N, Gammeltoft S, Brunak S: Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol 1999, 294(5):1351\u20131362. 10.1006\/jmbi.1999.3310","journal-title":"J Mol Biol"},{"issue":"4","key":"2847_CR17","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1002\/pro.5560040404","volume":"4","author":"SC Bagley","year":"1995","unstructured":"Bagley SC, Altman RB: Characterizing the microenvironment surrounding protein sites. Protein Sci 1995, 4(4):622\u2013635.","journal-title":"Protein Sci"},{"key":"2847_CR18","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4757-2440-0","volume-title":"The nature of statistical learning theory","author":"V Vapnik","year":"1995","unstructured":"Vapnik V: The nature of statistical learning theory. Springer-Verlag New York, Inc; 1995."},{"key":"2847_CR19","volume-title":"Advances in Kernel Methods: Support Vector Machines","author":"T Joachims","year":"1998","unstructured":"Joachims T, Sch\u00f6lkopf CB: Making large-scale support vector machine learning practical. In Advances in Kernel Methods: Support Vector Machines. MIT Press, Cambridge, MA; 1998."},{"issue":"1","key":"2847_CR20","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/j.compbiolchem.2004.11.001","volume":"29","author":"Y Wang","year":"2005","unstructured":"Wang Y, Tetko IV, Hall MA, Frank E, Facius A, Mayer KF, Mewes HW: Gene selection from microarray data for cancer classification \u2013 a machine learning approach. Comput Biol Chem 2005, 29(1):37\u201346. 10.1016\/j.compbiolchem.2004.11.001","journal-title":"Comput Biol Chem"},{"issue":"16","key":"2847_CR21","doi-asserted-by":"publisher","first-page":"2097","DOI":"10.1093\/bioinformatics\/btg288","volume":"19","author":"J Qin","year":"2003","unstructured":"Qin J, Lewis DP, Noble WS: Kernel hierarchical gene clustering from microarray expression data. Bioinformatics 2003, 19(16):2097\u20132104. 10.1093\/bioinformatics\/btg288","journal-title":"Bioinformatics"},{"issue":"Suppl 4","key":"2847_CR22","doi-asserted-by":"publisher","first-page":"S25","DOI":"10.1186\/1471-2105-7-S4-S25","volume":"7","author":"M Pirooznia","year":"2006","unstructured":"Pirooznia M, Deng Y: SVM Classifier \u2013 a comprehensive java interface for support vector machine classification of microarray data. BMC Bioinformatics 2006, 7(Suppl 4):S25. 10.1186\/1471-2105-7-S4-S25","journal-title":"BMC Bioinformatics"},{"key":"2847_CR23","first-page":"649","volume-title":"Proc Symp Biocomput","author":"JP Vert","year":"2002","unstructured":"Vert JP: Support vector machine prediction of signal peptide cleavage site using a new class of kernels for strings. Proc Symp Biocomput 2002, 649\u2013660."},{"issue":"9","key":"2847_CR24","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1093\/bioinformatics\/16.9.799","volume":"16","author":"A Zien","year":"2000","unstructured":"Zien A, Ratsch G, Mika S, Scholkopf B, Lengauer T, Muller KR: Engineering support vector machine kernels that recognize translation initiation sites. Bioinformatics 2000, 16(9):799\u2013807. 10.1093\/bioinformatics\/16.9.799","journal-title":"Bioinformatics"},{"issue":"1","key":"2847_CR25","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1016\/S0097-8485(01)00094-8","volume":"26","author":"R Burbidge","year":"2001","unstructured":"Burbidge R, Trotter M, Buxton B, Holden S: Drug design by machine learning: support vector machines for pharmaceutical data analysis. Comput Chem 2001, 26(1):5\u201314. 10.1016\/S0097-8485(01)00094-8","journal-title":"Comput Chem"},{"issue":"4","key":"2847_CR26","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1093\/bioinformatics\/17.4.349","volume":"17","author":"CH Ding","year":"2001","unstructured":"Ding CH, Dubchak I: Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics 2001, 17(4):349\u2013358. 10.1093\/bioinformatics\/17.4.349","journal-title":"Bioinformatics"},{"key":"2847_CR27","doi-asserted-by":"crossref","unstructured":"Heazlewood JL, Durek P, Hummel J, Selbig J, Weckwerth W, Walther D, Schulze WX: PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Res 2008, (36 Database):D1015\u20131021.","DOI":"10.1093\/nar\/gkm812"},{"issue":"20","key":"2847_CR28","doi-asserted-by":"publisher","first-page":"6097","DOI":"10.1093\/nar\/18.20.6097","volume":"18","author":"TD Schneider","year":"1990","unstructured":"Schneider TD, Stephens RM: Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 1990, 18(20):6097\u20136100. 10.1093\/nar\/18.20.6097","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"2847_CR29","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1016\/0092-8674(87)90509-5","volume":"50","author":"T Hunter","year":"1987","unstructured":"Hunter T: A thousand and one protein kinases. Cell 1987, 50(6):823\u2013829. 10.1016\/0092-8674(87)90509-5","journal-title":"Cell"},{"issue":"5600","key":"2847_CR30","doi-asserted-by":"publisher","first-page":"1912","DOI":"10.1126\/science.1075762","volume":"298","author":"G Manning","year":"2002","unstructured":"Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S: The protein kinase complement of the human genome. Science 2002, 298(5600):1912\u20131934. 10.1126\/science.1075762","journal-title":"Science"},{"issue":"1","key":"2847_CR31","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1093\/nar\/27.1.237","volume":"27","author":"A Kreegipuu","year":"1999","unstructured":"Kreegipuu A, Blom N, Brunak S: PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic Acids Res 1999, 27(1):237\u2013239. 10.1093\/nar\/27.1.237","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"2847_CR32","doi-asserted-by":"publisher","first-page":"1391","DOI":"10.1038\/nbt1146","volume":"23","author":"D Schwartz","year":"2005","unstructured":"Schwartz D, Gygi SP: An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat Biotechnol 2005, 23(11):1391\u20131398. 10.1038\/nbt1146","journal-title":"Nat Biotechnol"},{"issue":"12","key":"2847_CR33","doi-asserted-by":"publisher","first-page":"1100","DOI":"10.1038\/70033","volume":"6","author":"K Niefind","year":"1999","unstructured":"Niefind K, Putter M, Guerra B, Issinger OG, Schomburg D: GTP plus water mimic ATP in the active site of protein kinase CK2. Nat Struct Biol 1999, 6(12):1100\u20131103. 10.1038\/70033","journal-title":"Nat Struct Biol"},{"issue":"4","key":"2847_CR34","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1016\/S0958-1669(02)00339-7","volume":"13","author":"U Reimer","year":"2002","unstructured":"Reimer U, Reineke U, Schneider-Mergener J: Peptide arrays: from macro to micro. Curr Opin Biotechnol 2002, 13(4):315\u2013320. 10.1016\/S0958-1669(02)00339-7","journal-title":"Curr Opin Biotechnol"},{"issue":"2","key":"2847_CR35","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1016\/j.jmb.2003.12.052","volume":"336","author":"L Rychlewski","year":"2004","unstructured":"Rychlewski L, Kschischo M, Dong L, Schutkowski M, Reimer U: Target specificity analysis of the Abl kinase using peptide microarray data. J Mol Biol 2004, 336(2):307\u2013311. 10.1016\/j.jmb.2003.12.052","journal-title":"J Mol Biol"},{"key":"2847_CR36","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/1471-2091-6-22","volume":"6","author":"AS Mah","year":"2005","unstructured":"Mah AS, Elia AE, Devgan G, Ptacek J, Schutkowski M, Snyder M, Yaffe MB, Deshaies RJ: Substrate specificity analysis of protein kinase complex Dbf2-Mob1 by peptide library and proteome array screening. BMC Biochem 2005, 6: 22. 10.1186\/1471-2091-6-22","journal-title":"BMC Biochem"},{"issue":"11","key":"2847_CR37","doi-asserted-by":"publisher","first-page":"1453","DOI":"10.1016\/j.str.2003.10.002","volume":"11","author":"R Linding","year":"2003","unstructured":"Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB: Protein disorder prediction: implications for structural proteomics. Structure 2003, 11(11):1453\u20131459. 10.1016\/j.str.2003.10.002","journal-title":"Structure"},{"issue":"11","key":"2847_CR38","doi-asserted-by":"publisher","first-page":"R250","DOI":"10.1186\/gb-2007-8-11-r250","volume":"8","author":"F Gnad","year":"2007","unstructured":"Gnad F, Ren S, Cox J, Olsen JV, Macek B, Oroshi M, Mann M: PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol 2007, 8(11):R250. 10.1186\/gb-2007-8-11-r250","journal-title":"Genome Biol"},{"issue":"6","key":"2847_CR39","doi-asserted-by":"publisher","first-page":"1011","DOI":"10.1016\/j.str.2006.04.006","volume":"14","author":"T Zhou","year":"2006","unstructured":"Zhou T, Sun L, Humphreys J, Goldsmith EJ: Docking interactions induce exposure of activation loop in the MAP kinase ERK2. Structure 2006, 14(6):1011\u20131019. 10.1016\/j.str.2006.04.006","journal-title":"Structure"},{"issue":"7068","key":"2847_CR40","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/nature04187","volume":"438","author":"J Ptacek","year":"2005","unstructured":"Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, et al.: Global analysis of protein phosphorylation in yeast. Nature 2005, 438(7068):679\u2013684. 10.1038\/nature04187","journal-title":"Nature"},{"issue":"3","key":"2847_CR41","doi-asserted-by":"publisher","first-page":"516","DOI":"10.1016\/S0006-291X(03)01182-3","volume":"307","author":"W Weckwerth","year":"2003","unstructured":"Weckwerth W, Selbig J: Scoring and identifying organism-specific functional patterns and putative phosphorylation sites in protein sequences using mutual information. Biochem Biophys Res Commun 2003, 307(3):516\u2013521. 10.1016\/S0006-291X(03)01182-3","journal-title":"Biochem Biophys Res Commun"},{"issue":"32","key":"2847_CR42","doi-asserted-by":"publisher","first-page":"23167","DOI":"10.1074\/jbc.M600480200","volume":"281","author":"KY Cheng","year":"2006","unstructured":"Cheng KY, Noble ME, Skamnaki V, Brown NR, Lowe ED, Kontogiannis L, Shen K, Cole PA, Siligardi G, Johnson LN: The role of the phospho-CDK2\/cyclin A recruitment site in substrate recognition. J Biol Chem 2006, 281(32):23167\u201323179. 10.1074\/jbc.M600480200","journal-title":"J Biol Chem"},{"issue":"6","key":"2847_CR43","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1016\/j.sbi.2006.10.008","volume":"16","author":"A Remenyi","year":"2006","unstructured":"Remenyi A, Good MC, Lim WA: Docking interactions in protein kinase and phosphatase networks. Curr Opin Struct Biol 2006, 16(6):676\u2013685. 10.1016\/j.sbi.2006.10.008","journal-title":"Curr Opin Struct Biol"},{"issue":"1","key":"2847_CR44","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1093\/nar\/gkg095","volume":"31","author":"B Boeckmann","year":"2003","unstructured":"Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, et al.: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003, 31(1):365\u2013370. 10.1093\/nar\/gkg095","journal-title":"Nucleic Acids Res"},{"issue":"4861","key":"2847_CR45","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1126\/science.3291115","volume":"241","author":"SK Hanks","year":"1988","unstructured":"Hanks SK, Quinn AM, Hunter T: The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Science 1988, 241(4861):42\u201352. 10.1126\/science.3291115","journal-title":"Science"},{"issue":"22","key":"2847_CR46","doi-asserted-by":"publisher","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"JD Thompson","year":"1994","unstructured":"Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673\u20134680. 10.1093\/nar\/22.22.4673","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"2847_CR47","first-page":"525","volume":"12","author":"RW Hooft","year":"1996","unstructured":"Hooft RW, Sander C, Scharf M, Vriend G: The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. Comput Appl Biosci 1996, 12(6):525\u2013529.","journal-title":"Comput Appl Biosci"},{"issue":"1","key":"2847_CR48","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1002\/prot.340090107","volume":"9","author":"C Sander","year":"1991","unstructured":"Sander C, Schneider R: Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 1991, 9(1):56\u201368. 10.1002\/prot.340090107","journal-title":"Proteins"},{"issue":"12","key":"2847_CR49","doi-asserted-by":"publisher","first-page":"2577","DOI":"10.1002\/bip.360221211","volume":"22","author":"W Kabsch","year":"1983","unstructured":"Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577\u20132637. 10.1002\/bip.360221211","journal-title":"Biopolymers"},{"key":"2847_CR50","unstructured":"PDBFINDER II database[ ftp:\/\/ftp.cmbi.ru.nl\/pub\/molbio\/data\/pdbfinder2\/ ]"},{"issue":"4","key":"2847_CR51","doi-asserted-by":"publisher","first-page":"895","DOI":"10.1002\/prot.21025","volume":"64","author":"Y Park","year":"2006","unstructured":"Park Y, Helms V: Assembly of transmembrane helices of simple polytopic membrane proteins from sequence conservation patterns. Proteins 2006, 64(4):895\u2013905. 10.1002\/prot.21025","journal-title":"Proteins"},{"issue":"20","key":"2847_CR52","doi-asserted-by":"publisher","first-page":"4277","DOI":"10.1021\/bi00613a026","volume":"17","author":"M Levitt","year":"1978","unstructured":"Levitt M: Conformational preferences of amino acids in globular proteins. Biochemistry 1978, 17(20):4277\u20134285. 10.1021\/bi00613a026","journal-title":"Biochemistry"},{"issue":"9","key":"2847_CR53","first-page":"1","volume":"11","author":"K Alexandros","year":"2004","unstructured":"Alexandros K, Alexandros S, Kurt H, Achim Z: kernlab \u2013 An S4 Package for Kernel Methods in R. Journal of Statistical Software 2004, 11(9):1\u201320.","journal-title":"Journal of Statistical Software"},{"issue":"3","key":"2847_CR54","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1148\/radiology.148.3.6878708","volume":"148","author":"JA Hanley","year":"1983","unstructured":"Hanley JA, McNeil BJ: A method of comparing the areas under receiver operating characteristic curves derived from the same cases. Radiology 1983, 148(3):839\u2013843.","journal-title":"Radiology"},{"issue":"1","key":"2847_CR55","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1093\/nar\/28.1.374","volume":"28","author":"S Kawashima","year":"2000","unstructured":"Kawashima S, Kanehisa M: AAindex: amino acid index database. Nucleic Acids Res 2000, 28(1):374. 10.1093\/nar\/28.1.374","journal-title":"Nucleic Acids Res"},{"key":"2847_CR56","doi-asserted-by":"crossref","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\u2013594. 10.1093\/nar\/gkm322","DOI":"10.1093\/nar\/gkm322"},{"key":"2847_CR57","unstructured":"DisPhos 1.3[ http:\/\/core.ist.temple.edu\/pred\/pred\/predict ]"},{"key":"2847_CR58","unstructured":"KinasePhos 2.0[ http:\/\/kinasephos2.mbc.nctu.edu.tw\/ ]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-117.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-10-117\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-117.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,19]],"date-time":"2019-05-19T12:14:20Z","timestamp":1558268060000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-117"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,4,21]]},"references-count":58,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["2847"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-117","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,4,21]]},"article-number":"117"}}