{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T14:34:45Z","timestamp":1772634885222,"version":"3.50.1"},"reference-count":64,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2009,10,8]],"date-time":"2009-10-08T00:00:00Z","timestamp":1254960000000},"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\/1471-2105-10-323","type":"journal-article","created":{"date-parts":[[2009,10,8]],"date-time":"2009-10-08T18:15:15Z","timestamp":1255025715000},"source":"Crossref","is-referenced-by-count":26,"title":["A stochastic context free grammar based framework for analysis of protein sequences"],"prefix":"10.1186","volume":"10","author":[{"given":"Witold","family":"Dyrka","sequence":"first","affiliation":[]},{"given":"Jean-Christophe","family":"Nebel","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,10,8]]},"reference":[{"issue":"3","key":"3053_CR1","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1109\/TIT.1956.1056813","volume":"2","author":"N Chomsky","year":"1956","unstructured":"Chomsky N: Three models for the description of language. IRE Trans. on Information Theory IT 1956, 2(3):113\u2013124. 10.1109\/TIT.1956.1056813","journal-title":"IRE Trans. on Information Theory IT"},{"key":"3053_CR2","doi-asserted-by":"publisher","first-page":"2561","DOI":"10.1093\/nar\/12.5.2561","volume":"12","author":"V Brendel","year":"1984","unstructured":"Brendel V, Busse HG: Genome structure described by formal languages. Nucleic Acid Res 1984, 12: 2561\u20132568. 10.1093\/nar\/12.5.2561","journal-title":"Nucleic Acid Res"},{"key":"3053_CR3","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1007\/BF02459508","volume":"46","author":"MA Jimenez-Montao","year":"1984","unstructured":"Jimenez-Montao MA: On the syntactic structure of protein sequences and the concept of grammar complexity. Bull Math Biol 1984, 46: 641\u2013659.","journal-title":"Bull Math Biol"},{"key":"3053_CR4","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1007\/BF02481771","volume":"49","author":"T Head","year":"1987","unstructured":"Head T: Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors. Bull Math Biol 1987, 49: 737\u2013750.","journal-title":"Bull Math Biol"},{"key":"3053_CR5","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1038\/nature01255","volume":"420","author":"DB Searls","year":"2002","unstructured":"Searls DB: The language of genes. Nature 2002, 420: 211\u2013217. 10.1038\/nature01255","journal-title":"Nature"},{"key":"3053_CR6","volume-title":"Proceedings of Intelligent Systems in Molecular Biology: 3-7 August 2002","author":"S Lonardi","year":"2002","unstructured":"Lonardi S: Pattern Discovery in Biosequences (tutorial). In Proceedings of Intelligent Systems in Molecular Biology: 3\u20137 August 2002. Edmonton, Canada; 2002."},{"issue":"1","key":"3053_CR7","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1142\/S0218213004001429","volume":"13","author":"I Jonyer","year":"2004","unstructured":"Jonyer I, Holder LB, Cook DJ: MDL-Based Context-Free Graph Grammar Induction and Applications. International Journal of Artificial Intelligence Tools 2004, 13(1):65\u201379. 10.1142\/S0218213004001429","journal-title":"International Journal of Artificial Intelligence Tools"},{"key":"3053_CR8","volume-title":"MSc thesis","author":"J Maczka","year":"2004","unstructured":"Maczka J: Zastosowanie wnioskowania gramatycznego w analizie biologicznych sekwencji danych. In MSc thesis. Wroclaw University of Technology; 2004."},{"key":"3053_CR9","first-page":"1651","volume-title":"Proceedings of the Thirty-Eighth Asilomar Conference on Signals, Systems and Computers: 2004","author":"PP Vaidyanathan","year":"2004","unstructured":"Vaidyanathan PP, Yoon BY: HMM with auxiliary memory: a new tool for modeling RNA secondary structures. In Proceedings of the Thirty-Eighth Asilomar Conference on Signals, Systems and Computers: 2004. Volume 2. IEEE Press, Monterey, CA; 2004:1651\u20131655."},{"issue":"7","key":"3053_CR10","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1109\/TPAMI.2005.140","volume":"27","author":"Y Sakakibara","year":"2005","unstructured":"Sakakibara Y: Grammatical Inference in Bioinformatics. IEEE Trans. On Pattern Analysis And Machine Intelligence 2005, 27(7):1051\u20131062. 10.1109\/TPAMI.2005.140","journal-title":"IEEE Trans. On Pattern Analysis And Machine Intelligence"},{"key":"3053_CR11","volume-title":"Proceedings of Genome Informatics Workshop: 1995","author":"T Ishikawa","year":"1995","unstructured":"Ishikawa T, Mitaku S, Terano T, Hirokawa T, Suwa M, Ching SB: Building a Knowledge-Base for Protein Function Prediction using Multistrategy Learning. In Proceedings of Genome Informatics Workshop: 1995. Edited by: Hagiya M, Suyama A, Takagi T, Nakai K, Miyano S, Yokomori T. Universal Academy Press, Tokyo; 1995."},{"issue":"3","key":"3053_CR12","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1093\/bib\/3.3.265","volume":"3","author":"CJA Sigrist","year":"2002","unstructured":"Sigrist CJA, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P: PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform 2002, 3(3):265\u2013274. 10.1093\/bib\/3.3.265","journal-title":"Brief Bioinform"},{"issue":"17","key":"3053_CR13","first-page":"3590","volume":"22","author":"TK Attwood","year":"1994","unstructured":"Attwood TK, Beck ME, Bleasby AJ, Parry-Smith DJ: PRINTS - A database of protein motif fingerprints. Nucleic Acids Res 1994, 22(17):3590\u20133596.","journal-title":"Nucleic Acids Res"},{"key":"3053_CR14","doi-asserted-by":"publisher","first-page":"D224","DOI":"10.1093\/nar\/gkl841","volume":"35","author":"NJ Mulder","year":"2007","unstructured":"Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Binns D, Bork P, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Haft D, Hulo N, Hunter S, Kanapin A, Kejariwal A, Labarga A: New developments in the InterPro database. Nucleic Acids Res 2007, 35: D224-D228. 10.1093\/nar\/gkl841","journal-title":"Nucleic Acids Res"},{"key":"3053_CR15","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1006\/jmbi.1994.1104","volume":"235","author":"A Krogh","year":"1994","unstructured":"Krogh A, Brown M, Mian IS, Sjolander K, Haussler D: Hidden Markov models in computational biology: Applications to protein modeling. J Mol Biol 1994, 235: 1501\u20131531. 10.1006\/jmbi.1994.1104","journal-title":"J Mol Biol"},{"key":"3053_CR16","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological analysis: sequence probabilistic models of proteins and nucleic acids","author":"R Durbin","year":"1998","unstructured":"Durbin R, Eddy SR, Krogh A, Mitchison G: Biological analysis: sequence probabilistic models of proteins and nucleic acids. Cambridge and New York: Cambridge University Press; 1998."},{"key":"3053_CR17","volume-title":"Inductive and Statistical Learning of Formal Grammars","author":"PR Dupont","year":"2002","unstructured":"Dupont PR: Inductive and Statistical Learning of Formal Grammars. Research talk at Universit\u00e9 catholique de Louvain, Louvain-La-Neuve; 2002."},{"key":"3053_CR18","volume-title":"International Encyclopedia of the Social & Behavioral Sciences","author":"S Geman","year":"2002","unstructured":"Geman S, Johnson M: Probabilistic grammars and their applications. In International Encyclopedia of the Social & Behavioral Sciences. Edited by: Smelser NJ, Baltes PB. Oxford: Pergamon; 2002."},{"key":"3053_CR19","first-page":"47","volume-title":"Artificial Intelligence and Molecular Biology","author":"DB Searls","year":"1993","unstructured":"Searls DB: The Computational Linguistics of Biological Sequences. In Artificial Intelligence and Molecular Biology. Volume 2. Edited by: Hunter L. AAAI Press, Menlo Park, CA; 1993:47\u2013120."},{"key":"3053_CR20","volume-title":"HMMER User's Guide: Biological sequence analysis using profile hidden Markov models","author":"S Eddy","year":"2003","unstructured":"Eddy S: HMMER User's Guide: Biological sequence analysis using profile hidden Markov models. Washington University School of Medicine, Howard Hughes Medical Institute and Dept. of Genetics; 2003."},{"key":"3053_CR21","doi-asserted-by":"publisher","first-page":"387","DOI":"10.3115\/992066.992129","volume-title":"Proceedings of the 14th conference on Computational linguistics","author":"J Kupiec","year":"1992","unstructured":"Kupiec J: An Algorithm for Estimating the Parameters of Unrestricted Hidden Stochastic Context-Free Grammars. In Proceedings of the 14th conference on Computational linguistics. Volume 1. Association for Computational Linguistics, Morristown, NJ; 1992:387\u2013393."},{"key":"3053_CR22","volume-title":"Proceedings of the 27th Hawaii Int. Conf. on System Sciences","author":"Y Sakakibara","year":"1993","unstructured":"Sakakibara Y, Brown M, Underwood RC, Mian IS: Stochastic Context-Free Grammars for Modeling RNA. In Proceedings of the 27th Hawaii Int. Conf. on System Sciences. Edited by: Hunter L. IEEE Computer, Los Alamitos, CA; 1993."},{"issue":"23","key":"3053_CR23","doi-asserted-by":"publisher","first-page":"5112","DOI":"10.1093\/nar\/22.23.5112","volume":"22","author":"Y Sakakibara","year":"1994","unstructured":"Sakakibara Y, Brown M, Hughey R, Mian IS, Sjolander K, Underwood R, Haussler D: Stochastic Context-Free Grammars for tRNA. Nucleic Acids Res 1994, 22(23):5112\u20135120. 10.1093\/nar\/22.23.5112","journal-title":"Nucleic Acids Res"},{"key":"3053_CR24","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1038\/nature05113","volume":"443","author":"KS Pollard","year":"2006","unstructured":"Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M, Vanderhaeghen P, Haussler D: An RNA gene expressed during cortical development evolved rapidly in humans. Nature 2006, 443: 167\u2013172. 10.1038\/nature05113","journal-title":"Nature"},{"key":"3053_CR25","doi-asserted-by":"crossref","unstructured":"Liu Q, Yang Y, Chen C, Bu J, Zhang Y, Ye X: RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure. BMC Bioinformatics 2008., 9(176):","DOI":"10.1186\/1471-2105-9-176"},{"issue":"5","key":"3053_CR26","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1016\/S0019-9958(67)91165-5","volume":"10","author":"EM Gold","year":"1967","unstructured":"Gold EM: Language identification in the limit. Information and Control 1967, 10(5):447\u2013474. 10.1016\/S0019-9958(67)91165-5","journal-title":"Information and Control"},{"key":"3053_CR27","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/0890-5401(92)90003-X","volume":"97","author":"Y Sakakibara","year":"1992","unstructured":"Sakakibara Y: Efficient learning of context-free grammars from positive structural examples. Inform Comput 1992, 97: 23\u201360. 10.1016\/0890-5401(92)90003-X","journal-title":"Inform Comput"},{"key":"3053_CR28","volume-title":"Introduction to Formal Languages","author":"GE Revesz","year":"1983","unstructured":"Revesz GE: Introduction to Formal Languages. New York: McGraw-Hill Book Company; 1983."},{"key":"3053_CR29","first-page":"547","volume-title":"Proceedings of the 97th Meeting of the Acoustical Society of America","author":"JK Baker","year":"1979","unstructured":"Baker JK: Trainable grammars for speech recognition. In Proceedings of the 97th Meeting of the Acoustical Society of America. Edited by: Klatt D, Wolf J. Acoustical Society of America; 1979:547\u2013550."},{"key":"3053_CR30","volume-title":"Introduction to Automata Theory, Languages, and Computation","author":"J Hopcroft","year":"1979","unstructured":"Hopcroft J, Ullman J: Introduction to Automata Theory, Languages, and Computation. Reading: Addison-Wesley; 1979."},{"issue":"1","key":"3053_CR31","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1214\/aoms\/1177697196","volume":"41","author":"LE Baum","year":"1970","unstructured":"Baum LE, Petrie T, Soules G, Weiss N: A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann Math Statist 1970, 41(1):164\u2013171. 10.1214\/aoms\/1177697196","journal-title":"Ann Math Statist"},{"issue":"3","key":"3053_CR32","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1109\/PROC.1973.9030","volume":"61","author":"GD Forney","year":"1973","unstructured":"Forney GD: The Viterbi algorithm. Proceedings of the IEEE 1973, 61(3):268\u2013278. 10.1109\/PROC.1973.9030","journal-title":"Proceedings of the IEEE"},{"key":"3053_CR33","volume-title":"Adaptation in Natural and Artificial Systems","author":"JH Holland","year":"1975","unstructured":"Holland JH: Adaptation in Natural and Artificial Systems. Ann Arbor: University of Michigan; 1975."},{"key":"3053_CR34","volume-title":"Genetic Algorithms in Search, Optimization and Machine Learning","author":"DE Goldberg","year":"1989","unstructured":"Goldberg DE: Genetic Algorithms in Search, Optimization and Machine Learning. Reading: Addison-Wesley; 1989."},{"key":"3053_CR35","volume-title":"Genetic Programming: On the Programming of Computers by Means of Natural Selection","author":"JR Koza","year":"1992","unstructured":"Koza JR: Genetic Programming: On the Programming of Computers by Means of Natural Selection. Cambridge: MIT Press; 1992."},{"issue":"2-3","key":"3053_CR36","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1023\/A:1007477814995","volume":"29","author":"N Abe","year":"1997","unstructured":"Abe N, Mamitsuka H: Predicting Protein Secondary Structure Using Stochastic Tree Grammars. Machine Learning 1997, 29(2\u20133):275\u2013301. 10.1023\/A:1007477814995","journal-title":"Machine Learning"},{"issue":"6","key":"3053_CR37","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1093\/bioinformatics\/15.6.446","volume":"15","author":"B Knudsen","year":"1999","unstructured":"Knudsen B, Hein J: RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 1999, 15(6):446\u2013454. 10.1093\/bioinformatics\/15.6.446","journal-title":"Bioinformatics"},{"key":"3053_CR38","volume-title":"Technical report","author":"M Mernik","year":"2003","unstructured":"Mernik M, Crepinsek M, Gerlic G, Zumer V, Viljem Z, Bryant BR, Sprague A: Learning Context-Free Grammars using an Evolutionary Approach. In Technical report. University of Maribor and the University of Alabama at Birmingham; 2003."},{"key":"3053_CR39","doi-asserted-by":"publisher","first-page":"1372","DOI":"10.1016\/j.patcog.2004.03.021","volume":"38","author":"Y Sakakibara","year":"2005","unstructured":"Sakakibara Y: Learning context-free grammars using tabular representations. Pattern Recognition 2005, 38: 1372\u20131383. 10.1016\/j.patcog.2004.03.021","journal-title":"Pattern Recognition"},{"key":"3053_CR40","doi-asserted-by":"publisher","first-page":"1393","DOI":"10.1016\/j.patcog.2004.03.022","volume":"38","author":"B Keller","year":"2005","unstructured":"Keller B, Lutz R: Evolutionary induction of stochastic context free grammars. Pattern Recognition 2005, 38: 1393\u20131406. 10.1016\/j.patcog.2004.03.022","journal-title":"Pattern Recognition"},{"key":"3053_CR41","volume-title":"MSc thesis","author":"W Dyrka","year":"2005","unstructured":"Dyrka W: Rozpoznawanie wzorc\u00f3w proteinowych z zastosowaniem metod maszynowego uczenia. In MSc thesis. Wroclaw University of Technology; 2005."},{"key":"3053_CR42","volume-title":"MSc thesis","author":"D Wadowski","year":"2004","unstructured":"Wadowski D: Zastosowanie ewolucyjnie modyfikowanych Maszyn Turinga w rozpoznawaniu biosekwencji. In MSc thesis. Wroclaw University of Technology; 2004."},{"key":"3053_CR43","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1093\/protein\/2.2.93","volume":"2","author":"K Nakai","year":"1998","unstructured":"Nakai K, Kidera A, Kanehisa M: Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng 1998, 2: 93\u2013100. 10.1093\/protein\/2.2.93","journal-title":"Protein Eng"},{"key":"3053_CR44","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/protein\/9.1.27","volume":"9","author":"K Tomii","year":"1996","unstructured":"Tomii K, Kanehisa M: Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng 1996, 9: 27\u201336. 10.1093\/protein\/9.1.27","journal-title":"Protein Eng"},{"key":"3053_CR45","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1093\/nar\/27.1.368","volume":"27","author":"S Kawashima","year":"1999","unstructured":"Kawashima S, Ogata H, Kanehisa M: AAindex: amino acid index database. Nucleic Acids Res 1999, 27: 368\u2013369. 10.1093\/nar\/27.1.368","journal-title":"Nucleic Acids Res"},{"key":"3053_CR46","doi-asserted-by":"publisher","first-page":"1617","DOI":"10.1002\/bip.1980.360190906","volume":"19","author":"MI Kanehisa","year":"1980","unstructured":"Kanehisa MI, Tsong TY: Local hydrophobicity stabilizes secondary structures in proteins. Biopolymers 1980, 19: 1617\u20131628. 10.1002\/bip.1980.360190906","journal-title":"Biopolymers"},{"key":"3053_CR47","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/S0022-2836(76)80008-3","volume":"107","author":"B Robson","year":"1976","unstructured":"Robson B, Suzuki E: Conformational properties of amino acid residues in globular proteins. J Mol Biol 1976, 107: 327\u2013356. 10.1016\/S0022-2836(76)80008-3","journal-title":"J Mol Biol"},{"key":"3053_CR48","first-page":"275","volume":"8","author":"DT Jones","year":"1992","unstructured":"Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Computer Applications in Biosciences 1992, 8: 275\u2013282.","journal-title":"Computer Applications in Biosciences"},{"key":"3053_CR49","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1111\/j.1399-3011.1988.tb01261.x","volume":"32","author":"JL Fauchere","year":"1988","unstructured":"Fauchere JL, Charton M, Kier LB, Verloop A, Pliska V: Amino acid side chain parameters for correlation studies in biology and pharmacology. Int J Peptide Protein Res 1988, 32: 269\u2013278.","journal-title":"Int J Peptide Protein Res"},{"key":"3053_CR50","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1093\/protein\/2.3.185","volume":"2","author":"V Biou","year":"1988","unstructured":"Biou V, Gibrat JF, Levin JM, Robson B, Garnier J: Secondary structure prediction: combination of three different methods. Protein Eng 1988, 2: 185\u2013191. 10.1093\/protein\/2.3.185","journal-title":"Protein Eng"},{"key":"3053_CR51","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1016\/0167-4838(84)90312-1","volume":"787","author":"P Klein","year":"1984","unstructured":"Klein P, Kanehisa M, DeLisi C: Prediction of protein function from sequence properties: Discriminant analysis of a data base. Biochim Biophys Acta 1984, 787: 221\u2013226.","journal-title":"Biochim Biophys Acta"},{"issue":"1","key":"3053_CR52","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1002\/prot.20288","volume":"58","author":"A Golovin","year":"2005","unstructured":"Golovin A, Dimitropoulos D, Oldfield T, Rachedi A, Henrick K: MSDsite: A Database Search and Retrieval System for the Analysis and Viewing of Bound Ligands and Active Sites. PROTEINS: Structure, Function, and Bioinformatics 2005, 58(1):190\u20139. 10.1002\/prot.20288","journal-title":"PROTEINS: Structure, Function, and Bioinformatics"},{"key":"3053_CR53","volume-title":"Wyk\u0142ady z algorytm\u00f3w ewolucyjnych","author":"J Arabas","year":"2004","unstructured":"Arabas J: Wyk\u0142ady z algorytm\u00f3w ewolucyjnych. Warsaw: Wydawnictwo Naukowo-Techniczne; 2004."},{"key":"3053_CR54","volume-title":"GAlib library documentation (version 2.4.4)","author":"M Wall","year":"1999","unstructured":"Wall M: GAlib library documentation (version 2.4.4). Massachusetts Institute of Technology; 1999."},{"key":"3053_CR55","volume-title":"MSc thesis","author":"W Dyrka","year":"2007","unstructured":"Dyrka W: Probabilistic Context-Free Grammar for pattern detection in protein sequences. In MSc thesis. Kingston University, London; 2007."},{"key":"3053_CR56","doi-asserted-by":"publisher","first-page":"D245","DOI":"10.1093\/nar\/gkm977","volume":"36","author":"N Hulo","year":"2007","unstructured":"Hulo N, Bairoch A, Bulliard V, Cerutti L, Cuche B, De Castro E, Lachaize C, Langendijk-Genevaux PS, Sigrist CJA: The 20 years of PROSITE. Nucleic Acids Res 2007, 36: D245\u20139. 10.1093\/nar\/gkm977","journal-title":"Nucleic Acids Res"},{"key":"3053_CR57","doi-asserted-by":"publisher","first-page":"D193","DOI":"10.1093\/nar\/gkl929","volume":"35","author":"UniProt Consortium","year":"2007","unstructured":"UniProt Consortium: Universal Protein Resource (UniProt). Nucleic Acid Res 2007, 35: D193-D197. 10.1093\/nar\/gkl929","journal-title":"Nucleic Acid Res"},{"key":"3053_CR58","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TT, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acid Res 2000, 28: 235\u2013242. 10.1093\/nar\/28.1.235","journal-title":"Nucleic Acid Res"},{"key":"3053_CR59","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1093\/protein\/8.2.127","volume":"8","author":"AC Wallace","year":"1995","unstructured":"Wallace AC, Laskowski RA, Thornton JM: LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995, 8: 127\u2013134. 10.1093\/protein\/8.2.127","journal-title":"Protein Eng"},{"key":"3053_CR60","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1108\/eb026538","volume":"28","author":"CW Cleverdon","year":"1972","unstructured":"Cleverdon CW: On the inverse relationship of Recall and Precision. Journal of Documentation 1972, 28: 195\u2013201. 10.1108\/eb026538","journal-title":"Journal of Documentation"},{"key":"3053_CR61","volume-title":"Proceedings of the 23rd International Conference on Machine Learning","author":"J Davis","year":"2006","unstructured":"Davis J, Goadrich M: The Relationship between Precision-Recall and ROC Curves. In Proceedings of the 23rd International Conference on Machine Learning. ACM Press; 2006."},{"key":"3053_CR62","doi-asserted-by":"publisher","first-page":"13769","DOI":"10.1021\/bi970069s","volume":"36","author":"B Feng","year":"1997","unstructured":"Feng B, Gorin AA, Hingerty BE, Geacintov NE, Broyde S, Patel DJ: Structural alignment of the (+)-trans-anti-benzo[a]pyrene-dG adduct positioned opposite dC at a DNA template primer junction. Biochemistry 1997, 36: 13769\u201313779. 10.1021\/bi970069s","journal-title":"Biochemistry"},{"key":"3053_CR63","first-page":"276","volume-title":"Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology","author":"H Mamitsuka","year":"1994","unstructured":"Mamitsuka H, Abe N: Predicting location and structure of beta-sheet regions using stochastic tree grammars. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA; 1994:276\u2013284."},{"key":"3053_CR64","first-page":"45","volume":"47","author":"PY Chou","year":"1978","unstructured":"Chou PY, Fasman GD: Prediction of the secondary structure of proteins from their amino acid sequence. J Adv Enzymol 1978, 47: 45\u2013148.","journal-title":"J Adv Enzymol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-323.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-10-323\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-323.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T06:27:15Z","timestamp":1548224835000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-323"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,10,8]]},"references-count":64,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["3053"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-323","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,10,8]]},"article-number":"323"}}