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Math."},{"key":"ref54\/cit54","first-page":"15","volume":"1","author":"Lance G. N.","year":"1967","journal-title":"Aust. Comput. J."},{"key":"ref55\/cit55","doi-asserted-by":"crossref","unstructured":"Dagan, I.; Lee, L.; Pereira, F.Similarity-Based Methods for Word Sense Disambiguation, Proceedings of the 35th Annual Meeting of the Association for Computational Linguistics and Eighth Conference of the European Chapter of the Association for Computational Linguistics, Stroudsburg, PA, U.S.A., 1997; pp56\u201363.","DOI":"10.3115\/976909.979625"},{"key":"ref56\/cit56","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1214\/aoms\/1177729694","volume":"22","author":"Kullback S.","year":"1951","journal-title":"Ann. Math. Stat."},{"key":"ref57\/cit57","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1021\/ci200274q","volume":"51","author":"Neudert G.","year":"2011","journal-title":"J. Chem. Inf. 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D.","year":"2005","journal-title":"J. Mol. Biol."},{"key":"ref63\/cit63","doi-asserted-by":"crossref","first-page":"1712","DOI":"10.1110\/ps.12801","volume":"10","author":"Dym O.","year":"2001","journal-title":"Protein Sci."},{"key":"ref64\/cit64","doi-asserted-by":"crossref","first-page":"2082","DOI":"10.1021\/ci300550a","volume":"53","author":"Glinca S.","year":"2013","journal-title":"J. Chem. Inf. Model."},{"key":"ref65\/cit65","doi-asserted-by":"crossref","first-page":"2261","DOI":"10.1021\/ci500131x","volume":"54","author":"Schomburg K. T.","year":"2014","journal-title":"J. Chem. Inf. Model."},{"key":"ref66\/cit66","doi-asserted-by":"crossref","first-page":"D343","DOI":"10.1093\/nar\/gkr987","volume":"40","author":"Rawlings N. D.","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref67\/cit67","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1148\/radiology.143.1.7063747","volume":"143","author":"Hanley J. 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