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Chem."},{"key":"ref27\/cit27","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1016\/j.jmgm.2009.01.001","volume":"27","author":"Ballester P. J.","year":"2009","journal-title":"J. Mol. Graphics Modell."},{"key":"ref28\/cit28","doi-asserted-by":"crossref","first-page":"65","DOI":"10.4155\/fmc.10.280","volume":"3","author":"Ballester P. J.","year":"2011","journal-title":"Future Med. Chem."},{"key":"ref29\/cit29","doi-asserted-by":"crossref","first-page":"1653","DOI":"10.1002\/(SICI)1096-987X(19961115)17:14<1653::AID-JCC7>3.0.CO;2-K","volume":"17","author":"Grant J. A.","year":"1996","journal-title":"J. Comput. Chem."},{"key":"ref30\/cit30","volume-title":"ROCS","year":"2006"},{"key":"ref31\/cit31","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1016\/j.jmgm.2007.08.009","volume":"26","author":"Mak L.","year":"2008","journal-title":"J. Mol. 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F.","year":"2007","journal-title":"J. Chem. Inf. Model."},{"key":"ref53\/cit53","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1007\/s10822-007-9163-6","volume":"22","author":"Kirchmair J.","year":"2008","journal-title":"J. Comput.-Aided Mol. Des."},{"key":"ref54\/cit54","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1007\/s10822-008-9196-5","volume":"22","author":"Jain A. N.","year":"2008","journal-title":"J. Comput.-Aided Mol. Des."},{"key":"ref55\/cit55","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1021\/ci8003978","volume":"49","author":"Mackey M. D.","year":"2009","journal-title":"J. Chem. Inf. Model."},{"key":"ref56\/cit56","doi-asserted-by":"crossref","first-page":"2129","DOI":"10.1021\/ci100219f","volume":"50","author":"Marques J. M. C.","year":"2010","journal-title":"J. Chem. Inf. Model."},{"key":"ref57\/cit57","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1021\/ci600526a","volume":"47","author":"Swamidass S. 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