{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T16:21:00Z","timestamp":1762100460548},"reference-count":28,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2006,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The structure of proteins may change as a result of the inherent flexibility of some protein regions. We develop and explore probabilistic machine learning methods for predicting a continuum secondary structure, i.e. assigning probabilities to the conformational states of a residue. We train our methods using data derived from high-quality NMR models.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Several probabilistic models not only successfully estimate the continuum secondary structure, but also provide a categorical output on par with models directly trained on categorical data. Importantly, models trained on the continuum secondary structure are also better than their categorical counterparts at identifying the conformational state for structurally ambivalent residues.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Cascaded probabilistic neural networks trained on the continuum secondary structure exhibit better accuracy in structurally ambivalent regions of proteins, while sustaining an overall classification accuracy on par with standard, categorical prediction methods.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-7-68","type":"journal-article","created":{"date-parts":[[2006,2,17]],"date-time":"2006-02-17T07:45:28Z","timestamp":1140162328000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures"],"prefix":"10.1186","volume":"7","author":[{"given":"Mikael","family":"Bod\u00e9n","sequence":"first","affiliation":[]},{"given":"Zheng","family":"Yuan","sequence":"additional","affiliation":[]},{"given":"Timothy L","family":"Bailey","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,2,14]]},"reference":[{"key":"807_CR1","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: 2577\u20132637. 10.1002\/bip.360221211","journal-title":"Biopolymers"},{"key":"807_CR2","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1016\/S0969-2126(02)00700-1","volume":"10","author":"CAF Andersen","year":"2002","unstructured":"Andersen CAF, Palmer AG, Brunak S, Rost B: Continuum secondary structure captures protein flexibility. Structure 2002, 10: 175\u2013184. 10.1016\/S0969-2126(02)00700-1","journal-title":"Structure"},{"issue":"13","key":"807_CR3","doi-asserted-by":"publisher","first-page":"3293","DOI":"10.1093\/nar\/gkg626","volume":"31","author":"P Carter","year":"2003","unstructured":"Carter P, Andersen CAF, Rost B: DSSPcont: continuous secondary structure assignments for proteins. Nucleic Acids Research 2003, 31(13):3293\u20133295. 10.1093\/nar\/gkg626","journal-title":"Nucleic Acids Research"},{"key":"807_CR4","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1006\/jmbi.1999.3091","volume":"292","author":"DT Jones","year":"1999","unstructured":"Jones DT: Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology 1999, 292: 195\u2013202. 10.1006\/jmbi.1999.3091","journal-title":"Journal of Molecular Biology"},{"key":"807_CR5","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1002\/prot.10082","volume":"47","author":"G Pollastri","year":"2002","unstructured":"Pollastri G, Przybylski D, Rost B, Baldi P: Improving the Prediction of Protein Secondary Strucure in Three and Eight Classes Using Recurrent Neural Networks and Profiles. Proteins: Structure, Function, and Genetics 2002, 47: 228\u2013235. 10.1002\/prot.10082","journal-title":"Proteins: Structure, Function, and Genetics"},{"key":"807_CR6","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1002\/1097-0134(20001001)41:1<17::AID-PROT40>3.0.CO;2-F","volume":"41","author":"T Nordahl-Petersen","year":"2000","unstructured":"Nordahl-Petersen T, Lundegaard C, Nielsen M, Bohr H, Bohr J, Brunak S, Gippert GP, Lund O: Prediction of protein secondary structure at 80% accuracy. Proteins: Structure, Function and Genetics 2000, 41: 17\u201320. Publisher Full Text 10.1002\/1097-0134(20001001)41:1<17::AID-PROT40>3.0.CO;2-F","journal-title":"Proteins: Structure, Function and Genetics"},{"issue":"2\u20133","key":"807_CR7","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1006\/jsbi.2001.4336","volume":"134","author":"B Rost","year":"2001","unstructured":"Rost B: Protein Secondary Structure Prediction Continues to Rise. Journal of Structural Biology 2001, 134(2\u20133):204\u2013218. 10.1006\/jsbi.2001.4336","journal-title":"Journal of Structural Biology"},{"issue":"2","key":"807_CR8","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1006\/jmbi.2001.4580","volume":"308","author":"S Hua","year":"2001","unstructured":"Hua S, Sun Z: A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach. Journal of Molecular Biology 2001, 308(2):397\u2013407. 10.1006\/jmbi.2001.4580","journal-title":"Journal of Molecular Biology"},{"issue":"13","key":"807_CR9","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1093\/bioinformatics\/btg223","volume":"19","author":"JJ Ward","year":"2003","unstructured":"Ward JJ, McGuffin LJ, Buxton BF, Jones DT: Secondary structure prediction with support vector machines. Bioinformatics 2003, 19(13):1650\u20131655. 10.1093\/bioinformatics\/btg223","journal-title":"Bioinformatics"},{"issue":"2","key":"807_CR10","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1016\/j.polymer.2003.10.065","volume":"45","author":"AD Solis","year":"2004","unstructured":"Solis AD, Rackovsky S: On the use of secondary structure in protein structure prediction: a bioinformatic analysis. Polymer 2004, 45(2):525\u2013546. 10.1016\/j.polymer.2003.10.065","journal-title":"Polymer"},{"key":"807_CR11","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1016\/j.neucom.2003.10.004","volume":"56","author":"Y Guermeur","year":"2004","unstructured":"Guermeur Y, Pollastri G, Elisseeff A, Zelus D, Paugam-Moisy H, Baldi P: Combining protein secondary structure prediction models with ensemble methods of optimal complexity. Neurocomputing 2004, 56: 305\u2013327. 10.1016\/j.neucom.2003.10.004","journal-title":"Neurocomputing"},{"issue":"4","key":"807_CR12","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1002\/prot.340230412","volume":"23","author":"D Frishman","year":"1995","unstructured":"Frishman D, Argos P: Knowledge-based protein secondary structure assignment. Proteins: Structure, Function, and Genetics 1995, 23(4):566\u2013579. 10.1002\/prot.340230412","journal-title":"Proteins: Structure, Function, and Genetics"},{"issue":"8","key":"807_CR13","doi-asserted-by":"publisher","first-page":"1955","DOI":"10.1110\/ps.051479505","volume":"14","author":"D Kihara","year":"2005","unstructured":"Kihara D: The effect of long-range interactions on the secondary structure formation of proteins. Protein Sci 2005, 14(8):1955\u20131963. 10.1110\/ps.051479505","journal-title":"Protein Sci"},{"issue":"2\u20133","key":"807_CR14","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1023\/A:1007413511361","volume":"29","author":"P Domingos","year":"1997","unstructured":"Domingos P, Pazzani M: On the optimality of the simple Bayesian classifier under zero-one loss. Machine Learning 1997, 29(2\u20133):103\u2013130. 10.1023\/A:1007413511361","journal-title":"Machine Learning"},{"key":"807_CR15","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1006\/jmbi.1993.1413","volume":"232","author":"B Rost","year":"1993","unstructured":"Rost B, Sander C: Prediction of Protein Secondary Structure at Better than 70% Accuracy. Journal of Molecular Biology 1993, 232: 584\u2013599. 10.1006\/jmbi.1993.1413","journal-title":"Journal of Molecular Biology"},{"key":"807_CR16","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1002\/(SICI)1097-0134(19990201)34:2<220::AID-PROT7>3.0.CO;2-K","volume":"34","author":"A Zemla","year":"1999","unstructured":"Zemla A, Venclovas C, Fidelis K, Rost B: A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment. Proteins 1999, 34: 220\u2013223. 10.1002\/(SICI)1097-0134(19990201)34:2<220::AID-PROT7>3.0.CO;2-K","journal-title":"Proteins"},{"key":"807_CR17","doi-asserted-by":"publisher","first-page":"548","DOI":"10.1002\/prot.10534","volume":"53","author":"VA Eyrich","year":"2003","unstructured":"Eyrich VA, Przybylski D, Koh IYY, Grana O, Pazos F, Valencia A, Rost B: CAFASP3 in the spotlight of EVA. Proteins: Structure, Function, and Genetics 2003, 53: 548\u2013560. 10.1002\/prot.10534","journal-title":"Proteins: Structure, Function, and Genetics"},{"issue":"9","key":"807_CR18","doi-asserted-by":"publisher","first-page":"1752","DOI":"10.1110\/ps.8.9.1752","volume":"8","author":"M Young","year":"1999","unstructured":"Young M, Kirshenbaum K, Dill K, Highsmith S: Predicting conformational switches in proteins. Protein Sci 1999, 8(9):1752\u20131764.","journal-title":"Protein Sci"},{"issue":"4","key":"807_CR19","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1002\/prot.20375","volume":"58","author":"Z Yuan","year":"2005","unstructured":"Yuan Z, Bailey TL, Teasdale R: Prediction of protein B-factor profiles. Proteins: Structure, Function, and Bioinformatics 2005, 58(4):905\u2013912. 10.1002\/prot.20375","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"key":"807_CR20","volume-title":"Proceedings of the Eleventh Conference on Uncertainty in Artificial Intelligence","author":"GH John","year":"1995","unstructured":"John GH, Langley P: Estimating continuous distributions in Bayesian classifiers. In Proceedings of the Eleventh Conference on Uncertainty in Artificial Intelligence. San Mateo: Morgan Kaufmann Publishers; 1995."},{"key":"807_CR21","volume-title":"CRC Handbook of Computer Science","author":"MI Jordan","year":"1997","unstructured":"Jordan MI, Bishop C: Neural networks. In CRC Handbook of Computer Science. Edited by: Tucker AB. Boca Raton, FL: CRC Press; 1997."},{"key":"807_CR22","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1093\/nar\/26.1.316","volume":"26","author":"L Holm","year":"1998","unstructured":"Holm L, Sander C: Touring protein fold space with Dali\/FSSP. Nucleic Acids Research 1998, 26: 318\u2013321. 10.1093\/nar\/26.1.316","journal-title":"Nucleic Acids Research"},{"key":"807_CR23","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1002\/pro.5560010313","volume":"1","author":"U Hobohm","year":"1992","unstructured":"Hobohm U, Scharf M, Schneider R, Sander C: Selection of representative protein data sets. Protein Science 1992, 1: 409\u2013417.","journal-title":"Protein Science"},{"key":"807_CR24","doi-asserted-by":"publisher","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"2","author":"J Thompson","year":"1994","unstructured":"Thompson J, Higgins D, Gibson T: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 1994, 2: 4673\u20134680.","journal-title":"Nucleic Acids Research"},{"key":"807_CR25","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"H Berman","year":"2000","unstructured":"Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H, Shindyalov I, Bourne P: The Protein Data Bank. Nucleic Acids Research 2000, 28: 235\u2013242. 10.1093\/nar\/28.1.235","journal-title":"Nucleic Acids Research"},{"key":"807_CR26","unstructured":"DSSPcont[http:\/\/cubic.bioc.columbia.edu\/services\/DSSPcont]"},{"issue":"5","key":"807_CR27","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1093\/bioinformatics\/16.5.412","volume":"16","author":"P Baldi","year":"2000","unstructured":"Baldi P, Brunak S, Chauvin Y, Andersen CAF, Nielsen H: Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 2000, 16(5):412\u2013424. 10.1093\/bioinformatics\/16.5.412","journal-title":"Bioinformatics"},{"key":"807_CR28","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological Sequence Analysis","author":"R Durbin","year":"1998","unstructured":"Durbin R, Eddy SR, Krogh A, Mitchison G: Biological Sequence Analysis. Cambridge, England: Cambridge University Press; 1998."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-7-68.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T11:00:46Z","timestamp":1630494046000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-7-68"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,2,14]]},"references-count":28,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2006,12]]}},"alternative-id":["807"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-7-68","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,2,14]]},"assertion":[{"value":"22 June 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 February 2006","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 February 2006","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"68"}}