{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T00:53:39Z","timestamp":1775264019736,"version":"3.50.1"},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2007,9,21]],"date-time":"2007-09-21T00:00:00Z","timestamp":1190332800000},"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":[[2007,12]]},"DOI":"10.1186\/1471-2105-8-357","type":"journal-article","created":{"date-parts":[[2007,9,22]],"date-time":"2007-09-22T02:13:23Z","timestamp":1190427203000},"source":"Crossref","is-referenced-by-count":36,"title":["An evolutionary method for learning HMM structure: prediction of protein secondary structure"],"prefix":"10.1186","volume":"8","author":[{"given":"Kyoung-Jae","family":"Won","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Hamelryck","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam","family":"Pr\u00fcgel-Bennett","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anders","family":"Krogh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,9,21]]},"reference":[{"key":"1729_CR1","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1016\/0022-2836(74)90405-7","volume":"88","author":"VI Lim","year":"1974","unstructured":"Lim VI: Algorithms for prediction of alpha helices and structural regions in globular proteins. J Mol Biol 1974, 88: 873\u2013894. 10.1016\/0022-2836(74)90405-7","journal-title":"J Mol Biol"},{"key":"1729_CR2","first-page":"45","volume":"47","author":"PY Chow","year":"1978","unstructured":"Chow PY, Fasman GD: Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol 1978, 47: 45\u2013148.","journal-title":"Adv Enzymol"},{"key":"1729_CR3","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/0022-2836(78)90297-8","volume":"120","author":"J Garnier","year":"1978","unstructured":"Garnier J, Osguthorpe DJ, Robson B: Analysis and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 1978, 120: 97\u2013120. 10.1016\/0022-2836(78)90297-8","journal-title":"J Mol Biol"},{"key":"1729_CR4","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1016\/0022-2836(88)90564-5","volume":"202","author":"N Qian","year":"1988","unstructured":"Qian N, Sejnowski TJ: Predicting the secondary structure of globular proteins using neural network models. J Mol Biol 1988, 202: 865\u2013884. 10.1016\/0022-2836(88)90564-5","journal-title":"J Mol Biol"},{"key":"1729_CR5","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1016\/0022-2836(88)90564-5","volume":"202","author":"H Bohr","year":"1988","unstructured":"Bohr H, Bohr J, Brunak S, Cotterill R, Lautrup B, N\u00f8rskov L, Olsen O, Petersen S: Predicting the secondary structure of globular proteins using neural network models. J Mol Biol 1988, 202: 865\u2013884. 10.1016\/0022-2836(88)90564-5","journal-title":"J Mol Biol"},{"key":"1729_CR6","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. J Mol Biol 1993, 232: 584\u2013599. 10.1006\/jmbi.1993.1413","journal-title":"J Mol Biol"},{"key":"1729_CR7","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. J Mol Biol 1999, 292: 195\u2013202. 10.1006\/jmbi.1999.3091","journal-title":"J Mol Biol"},{"issue":"11","key":"1729_CR8","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1093\/bioinformatics\/15.11.937","volume":"15","author":"P Baldi","year":"1999","unstructured":"Baldi P, Brunak S, Frasconi P, Soda G, Pollastri G: Exploiting the past and the future in protein secondary structure prediction. Bioinformatics 1999, 15(11):937\u2013946. 10.1093\/bioinformatics\/15.11.937","journal-title":"Bioinformatics"},{"key":"1729_CR9","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 Structure in Three and Eight Classes Using Recurrent Neural Networks and Profiles. Proteins 2002, 47: 228\u2013235. 10.1002\/prot.10082","journal-title":"Proteins"},{"issue":"2","key":"1729_CR10","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1093\/bioinformatics\/bth487","volume":"21","author":"K Lin","year":"2005","unstructured":"Lin K, Simossis VA, Taylor WR, Heringa J: A simple and fast secondary structure prodiction method using hidden neural networks. Bioinformatics 2005, 21(2):152\u2013159. 10.1093\/bioinformatics\/bth487","journal-title":"Bioinformatics"},{"key":"1729_CR11","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. J Mol Biol 2001, 308: 397\u2013407. 10.1006\/jmbi.2001.4580","journal-title":"J Mol Biol"},{"issue":"13","key":"1729_CR12","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"},{"key":"1729_CR13","doi-asserted-by":"publisher","first-page":"738","DOI":"10.1002\/prot.10634","volume":"54","author":"J Guo","year":"2004","unstructured":"Guo J, Chen H, Sun Z, Lin Y: A Novel Method for Protein Secondary Structure Prediction Using Dual-Layer SVM and Profiles. Proteins 2004, 54: 738\u2013743. 10.1002\/prot.10634","journal-title":"Proteins"},{"key":"1729_CR14","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"24","author":"S Altschul","year":"1997","unstructured":"Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 1997, 24: 3389\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucl Acids Res"},{"key":"1729_CR15","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1002\/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO;2-Q","volume":"40","author":"J Cuff","year":"2000","unstructured":"Cuff J, Barton G: Application of Multiple Sequence Alignment Profiles to Improve Protein Secondary Structure Prediction. Proteins 2000, 40: 502\u2013511. 10.1002\/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO;2-Q","journal-title":"Proteins"},{"issue":"7","key":"1729_CR16","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1093\/protein\/gzg063","volume":"16","author":"M Albrecht","year":"2003","unstructured":"Albrecht M, Tosatto S, Lengauer T, Valle G: Simple consensus procedures are effective and sufficient in secondary structure prediction. Protein Eng 2003, 16(7):459\u2013462. 10.1093\/protein\/gzg063","journal-title":"Protein Eng"},{"key":"1729_CR17","first-page":"141","volume":"9","author":"K Asai","year":"1993","unstructured":"Asai K, Hayamnizu S, Handa K: Prediction of protein secondary structure by the hidden Markov model. Comput Appl Biosci 1993, 9: 141\u2013146.","journal-title":"Comput Appl Biosci"},{"issue":"13","key":"1729_CR18","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1002\/(SICI)1520-684X(19991130)30:13<13::AID-SCJ2>3.0.CO;2-7","volume":"30","author":"H Yoshikawa","year":"1999","unstructured":"Yoshikawa H, Ikeguchi M, Nakamura S, Shimizu K, Doi J: Prediction of Protein Structure Classes and Secondary Structure by Means of Hidden Markov Models. Systems and Computers in Japan 1999, 30(13):13\u201322. \n                    Publisher Full Text\n                    \n                   10.1002\/(SICI)1520-684X(19991130)30:13<13::AID-SCJ2>3.0.CO;2-7","journal-title":"Systems and Computers in Japan"},{"key":"1729_CR19","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1006\/jmbi.2000.3837","volume":"301","author":"C Bystroff","year":"2000","unstructured":"Bystroff C, Thorsson V, Baker D: HMMSTR: a Hidden Markov Model for Local Sequence-Structure Correlations in Proteins. J Mol Biol 2000, 301: 173\u2013190. 10.1006\/jmbi.2000.3837","journal-title":"J Mol Biol"},{"key":"1729_CR20","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1162\/089976699300016764","volume":"11","author":"A Krogh","year":"1999","unstructured":"Krogh A, Riis SK: Hidden Neural Networks. Neural Computation 1999, 11: 541\u2013563. 10.1162\/089976699300016764","journal-title":"Neural Computation"},{"issue":"18","key":"1729_CR21","doi-asserted-by":"publisher","first-page":"3613","DOI":"10.1093\/bioinformatics\/bth454","volume":"20","author":"KJ Won","year":"2004","unstructured":"Won KJ, Pr\u00fcgel-Bennett A, Krogh A: Training HMM Structure with Genetic Algorithms for Biological Sequence Analysis. Bioinformatics 2004, 20(18):3613\u20133627. 10.1093\/bioinformatics\/bth454","journal-title":"Bioinformatics"},{"key":"1729_CR22","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1109\/TEVC.2005.851271","volume":"10","author":"KJ Won","year":"2006","unstructured":"Won KJ, Pr\u00fcgel-Bennett A, Krogh A: Evolving the Structure of Hidden Markov Models. IEEE Transactions on Evolutionary Computation 2006, 10: 39\u201349. 10.1109\/TEVC.2005.851271","journal-title":"IEEE Transactions on Evolutionary Computation"},{"key":"1729_CR23","volume-title":"PhD thesis","author":"A Stolcke","year":"1994","unstructured":"Stolcke A: Bayesian Learning of Probabilistic Language Models. PhD thesis. University of California at Berkeley; 1994."},{"key":"1729_CR24","first-page":"121","volume-title":"ISMB1994","author":"Y Fujiwara","year":"1994","unstructured":"Fujiwara Y, Asogawa M, Konagaya A: Stochastic motif extraction using hidden Markov model. ISMB1994 1994, 121\u2013129."},{"key":"1729_CR25","first-page":"713","volume-title":"Pacific Symposium on Biocumputing '96","author":"Y Fujiwara","year":"1995","unstructured":"Fujiwara Y, Asogawa M, Konagaya A: Motif Extraction using an Improved Iterative Duplication Method for HMM Topology Learning. Pacific Symposium on Biocumputing '96 1995, 713\u2013714."},{"key":"1729_CR26","first-page":"178","volume":"5","author":"T Yada","year":"1994","unstructured":"Yada T, Ishikawa M, Tanaka H, Asai K: DNA Sequence Analysis using Hidden Markov Model and Genetic Algorithm. Genome Informatics 1994, 5: 178\u2013179.","journal-title":"Genome Informatics"},{"key":"1729_CR27","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1093\/bioinformatics\/14.4.317","volume":"14","author":"T Yada","year":"1998","unstructured":"Yada T, Totoki Y, Ishikawa M, Asai K, Nakai K: Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences. Bioinformatics 1998, 14: 317\u2013325. 10.1093\/bioinformatics\/14.4.317","journal-title":"Bioinformatics"},{"key":"1729_CR28","first-page":"750","volume":"40","author":"T Yada","year":"1995","unstructured":"Yada T: Generation of hidden Markov model describing complex motif in DNA sequences. IPSJ Trans 1995, 40: 750\u2013767.","journal-title":"IPSJ Trans"},{"key":"1729_CR29","volume-title":"PhD thesis","author":"T Yada","year":"1998","unstructured":"Yada T: Stochastic models representing DNA sequence data construction algorithms and their applications to prediction of gene structure and function. PhD thesis. University of Tokyo; 1998."},{"key":"1729_CR30","first-page":"861","volume":"2439","author":"R Thomsen","year":"2002","unstructured":"Thomsen R: Evolving the Topology of Hidden Markov Models Using Evolutionary Algorithms. LNCS 2002, 2439: 861\u2013870.","journal-title":"LNCS"},{"key":"1729_CR31","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1002\/prot.10051","volume":"5","author":"B Rost","year":"2001","unstructured":"Rost B, Eyrich V: EVA: large-scale analysis of secondary structure prediction. Proteins 2001, 5: 192\u2013199. 10.1002\/prot.10051","journal-title":"Proteins"},{"key":"1729_CR32","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1186\/1471-2105-7-178","volume":"7","author":"Z Aydin","year":"2006","unstructured":"Aydin Z, Altunbasak Y, Borodovsky M: Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. BMC Bioinformatics 2006, 7: 178. 10.1186\/1471-2105-7-178","journal-title":"BMC Bioinformatics"},{"key":"1729_CR33","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/1472-6807-6-25","volume":"6","author":"J Martin","year":"2006","unstructured":"Martin J, Gibrat JF, Rodolphe F: Analysis of an optimal hidden Markov model for secondary structure prediction. BMC Structural Biology 2006, 6: 25. 10.1186\/1472-6807-6-25","journal-title":"BMC Structural Biology"},{"issue":"7","key":"1729_CR34","doi-asserted-by":"publisher","first-page":"1267","DOI":"10.1093\/bioinformatics\/bth493","volume":"21","author":"I Van Walle","year":"2005","unstructured":"Van Walle I, Lasters I, Wyns L: SABmark \u2013 a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics 2005, 21(7):1267\u20131268. 10.1093\/bioinformatics\/bth493","journal-title":"Bioinformatics"},{"key":"1729_CR35","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":"1729_CR36","doi-asserted-by":"publisher","first-page":"2308","DOI":"10.1093\/bioinformatics\/btg299","volume":"19","author":"T Hamelryck","year":"2003","unstructured":"Hamelryck T, Manderick B: PDB file parser and structure class implemented in Python. Bioinformatics 2003, 19: 2308\u20132310. 10.1093\/bioinformatics\/btg299","journal-title":"Bioinformatics"},{"key":"1729_CR37","first-page":"14","volume-title":"Proceedings of the Second International Conference on Genetic Algorithms","author":"JE Baker","year":"1987","unstructured":"Baker JE: Reducing Bias and Inefficiency in the Selection Algorithm. In Proceedings of the Second International Conference on Genetic Algorithms. Lawrence Erlbaum Associates (Hillsdale); 1987:14\u201321."},{"key":"1729_CR38","first-page":"179","volume-title":"Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology","author":"A Krogh","year":"1997","unstructured":"Krogh A: Two methods for improving performance of an HMM and their application for gene finding. Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology 1997, 179\u2013186."},{"issue":"17","key":"1729_CR39","doi-asserted-by":"publisher","first-page":"3236","DOI":"10.1093\/bioinformatics\/bth191","volume":"20","author":"R Leinonen","year":"2004","unstructured":"Leinonen R, Diez F, Fleischmann W, Lopez R, Apweiler R: Uniprot archive. Bioinformatics 2004, 20(17):3236\u20133237. 10.1093\/bioinformatics\/bth191","journal-title":"Bioinformatics"},{"key":"1729_CR40","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1016\/0022-2836(94)90032-9","volume":"243","author":"S Henikoff","year":"1994","unstructured":"Henikoff S, Henikoff J: Position-based Sequence Weights. J Mol Biol 1994, 243: 574\u2013578. 10.1016\/0022-2836(94)90032-9","journal-title":"J Mol Biol"},{"key":"1729_CR41","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1038\/323533a0","volume":"323","author":"D Rumelhart","year":"1986","unstructured":"Rumelhart D, Hinton G, Williams R: Learning representations by back-propagating error. Nature 1986, 323: 533\u2013536. 10.1038\/323533a0","journal-title":"Nature"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-357.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-8-357\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-357.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T05:02:08Z","timestamp":1548219728000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-357"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,9,21]]},"references-count":41,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1729"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-357","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,9,21]]},"article-number":"357"}}