{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T02:16:59Z","timestamp":1772763419984,"version":"3.50.1"},"reference-count":63,"publisher":"American Chemical Society (ACS)","issue":"6","license":[{"start":{"date-parts":[[2015,5,16]],"date-time":"2015-05-16T00:00:00Z","timestamp":1431734400000},"content-version":"vor","delay-in-days":347,"URL":"http:\/\/pubs.acs.org\/page\/policy\/authorchoice_termsofuse.html"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["XSEDE-MCA01S027"],"award-info":[{"award-number":["XSEDE-MCA01S027"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01-GM081411"],"award-info":[{"award-number":["R01-GM081411"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001597","name":"Willard L. Eccles Charitable Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001597","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005496","name":"American Foundation for Pharmaceutical Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005496","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2014,6,23]]},"DOI":"10.1021\/ci500132c","type":"journal-article","created":{"date-parts":[[2014,5,16]],"date-time":"2014-05-16T18:13:46Z","timestamp":1400264026000},"page":"1758-1772","source":"Crossref","is-referenced-by-count":12,"title":["Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations"],"prefix":"10.1021","volume":"54","author":[{"given":"Niel M.","family":"Henriksen","sequence":"first","affiliation":[{"name":"Department of Medicinal Chemistry,\rCollege of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States"}]},{"given":"Hamed S.","family":"Hayatshahi","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry,\rCollege of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States"}]},{"given":"Darrell R.","family":"Davis","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry,\rCollege of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States"}]},{"suffix":"III","given":"Thomas E.","family":"Cheatham","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry,\rCollege of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States"}]}],"member":"316","published-online":{"date-parts":[[2014,6,3]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1038\/nrg2172","volume":"8","author":"Serganov A.","year":"2007","journal-title":"Nat. Rev. Genet."},{"key":"ref2\/cit2","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1042\/BST0390641","volume":"39","author":"Lilley D. M.","year":"2011","journal-title":"Biochem. Soc. Trans."},{"key":"ref3\/cit3","doi-asserted-by":"crossref","first-page":"1998","DOI":"10.1016\/j.biochi.2011.06.026","volume":"93","author":"Talini G.","year":"2011","journal-title":"Biochimie"},{"key":"ref4\/cit4","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1016\/S1367-5931(00)00142-3","volume":"4","author":"Sucheck S. J.","year":"2000","journal-title":"Curr. Opin. Chem. Biol."},{"key":"ref5\/cit5","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/S0307-4412(98)00289-1","volume":"27","author":"Claros M. G.","year":"1999","journal-title":"Biochem. Educ."},{"key":"ref6\/cit6","unstructured":"Rio, D. C.; Ares, M.; Nilsen, T. W.RNA: A Laboratory Manual;Cold Spring Harbor Laboratory Press:Cold Spring Harbor, NY, 2011; p586."},{"key":"ref7\/cit7","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1261\/rna.1563609","volume":"15","author":"Lang P. T.","year":"2009","journal-title":"RNA"},{"key":"ref8\/cit8","doi-asserted-by":"crossref","first-page":"2741","DOI":"10.1021\/ci300320t","volume":"52","author":"Chen L.","year":"2012","journal-title":"J. Chem. Inf. Model."},{"key":"ref9\/cit9","doi-asserted-by":"crossref","first-page":"117","DOI":"10.3851\/IMP1693","volume":"21","author":"Davis D. R.","year":"2011","journal-title":"Antiviral Chem. Chemother."},{"key":"ref10\/cit10","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1038\/nsb1004","volume":"10","author":"Lukavsky P. J.","year":"2003","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref11\/cit11","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1002\/ange.200603807","volume":"119","author":"Dibrov S. M.","year":"2007","journal-title":"Angew. Chem."},{"key":"ref12\/cit12","doi-asserted-by":"crossref","first-page":"7263","DOI":"10.1073\/pnas.0911896107","volume":"107","author":"Paulsen R. B.","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"ref13\/cit13","doi-asserted-by":"crossref","first-page":"5223","DOI":"10.1073\/pnas.1118699109","volume":"109","author":"Dibrov S. M.","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"ref14\/cit14","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1021\/cr0301088","volume":"105","author":"Magnet S.","year":"2005","journal-title":"Chem. Rev."},{"key":"ref15\/cit15","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1021\/cb3005116","volume":"8","author":"Becker B.","year":"2013","journal-title":"ACS Chem. Biol."},{"key":"ref16\/cit16","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1038\/sj.emboj.7601549","volume":"26","author":"Locker N.","year":"2007","journal-title":"EMBO J."},{"key":"ref17\/cit17","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.virusres.2008.06.004","volume":"139","author":"Lukavsky P. J.","year":"2009","journal-title":"Virus Res."},{"key":"ref18\/cit18","doi-asserted-by":"crossref","first-page":"7099","DOI":"10.1021\/jm050815o","volume":"48","author":"Seth P. P.","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref19\/cit19","doi-asserted-by":"crossref","first-page":"5489","DOI":"10.1529\/biophysj.108.131813","volume":"95","author":"Draper D. E.","year":"2008","journal-title":"Biophys. J."},{"key":"ref20\/cit20","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/j.sbi.2012.04.006","volume":"22","author":"Bowman J. C.","year":"2012","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref21\/cit21","first-page":"101","volume":"9","author":"Tan Z. J.","year":"2011","journal-title":"Met. Ions Life Sci."},{"key":"ref22\/cit22","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1016\/j.jmb.2009.04.083","volume":"390","author":"Lambert D.","year":"2009","journal-title":"J. Mol. Biol."},{"key":"ref23\/cit23","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1006\/jmbi.2000.4031","volume":"302","author":"Shiman R.","year":"2000","journal-title":"J. Mol. Biol."},{"key":"ref24\/cit24","doi-asserted-by":"crossref","first-page":"7821","DOI":"10.1039\/c0cp00111b","volume":"12","author":"Dupradeau F. Y.","year":"2010","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref25\/cit25","doi-asserted-by":"crossref","first-page":"1623","DOI":"10.1002\/jcc.10128","volume":"23","author":"Jakalian A.","year":"2002","journal-title":"J. Comput. Chem."},{"key":"ref26\/cit26","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1002\/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P","volume":"21","author":"Jakalian A.","year":"2000","journal-title":"J. Comput. Chem."},{"key":"ref27\/cit27","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/0039-9140(95)01789-5","volume":"43","author":"Hilal S.","year":"1996","journal-title":"Talanta"},{"key":"ref28\/cit28","doi-asserted-by":"crossref","first-page":"10269","DOI":"10.1021\/j100142a004","volume":"97","author":"Bayly C. I.","year":"1993","journal-title":"J. Phys. Chem."},{"key":"ref29\/cit29","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/0009-2614(95)01082-K","volume":"246","author":"Hawkins G. D.","year":"1995","journal-title":"Chem. Phys. Lett."},{"key":"ref30\/cit30","doi-asserted-by":"crossref","first-page":"2312","DOI":"10.1021\/ct700119m","volume":"3","author":"Shao J.","year":"2007","journal-title":"J. Chem. Theory Comput."},{"key":"ref31\/cit31","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1002\/jcc.20035","volume":"25","author":"Wang J.","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref32\/cit32","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.jmgm.2005.12.005","volume":"25","author":"Wang J.","year":"2006","journal-title":"J. Mol. Graphics Modell."},{"key":"ref33\/cit33","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1002\/jcc.20290","volume":"26","author":"Case D. A.","year":"2005","journal-title":"J. Comput. Chem."},{"key":"ref34\/cit34","doi-asserted-by":"crossref","first-page":"2886","DOI":"10.1021\/ct200162x","volume":"7","author":"Zgarbov\u00e1 M.","year":"2011","journal-title":"J. Chem. Theory Comput."},{"key":"ref35\/cit35","doi-asserted-by":"crossref","first-page":"3836","DOI":"10.1021\/ct100481h","volume":"6","author":"Ban\u00e1\u0161 P.","year":"2010","journal-title":"J. Chem. Theory Comput."},{"key":"ref36\/cit36","doi-asserted-by":"crossref","first-page":"3817","DOI":"10.1529\/biophysj.106.097782","volume":"92","author":"P\u00e9rez A.","year":"2007","journal-title":"Biophys. J."},{"key":"ref37\/cit37","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","author":"Jorgensen W. L.","year":"1983","journal-title":"J. Chem. Phys."},{"key":"ref38\/cit38","doi-asserted-by":"crossref","first-page":"9020","DOI":"10.1021\/jp8001614","volume":"112","author":"Joung I. S.","year":"2008","journal-title":"J. Phys. Chem. B"},{"key":"ref39\/cit39","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1021\/ct3000734","volume":"8","author":"Alln\u00e9r O.","year":"2012","journal-title":"J. Chem. Theory Comput."},{"key":"ref40\/cit40","first-page":"3684","volume":"81","author":"Berendsen H. J. C.","year":"1984","journal-title":"J. Comput. Phys."},{"key":"ref41\/cit41","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","volume":"23","author":"Ryckaert J. P.","year":"1977","journal-title":"J. Comput. Phys."},{"key":"ref42\/cit42","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","volume":"103","author":"Essmann U.","year":"1995","journal-title":"J. Chem. Phys."},{"key":"ref43\/cit43","doi-asserted-by":"crossref","first-page":"9401","DOI":"10.1021\/ja981844+","volume":"120","author":"Srinivasan J.","year":"1998","journal-title":"J. Am. Chem. Soc."},{"key":"ref44\/cit44","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1023\/A:1007930623000","volume":"12","author":"Hansson T.","year":"1998","journal-title":"J. Comput.-Aided Mol. Des."},{"key":"ref45\/cit45","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/S0301-4622(98)00230-0","volume":"78","author":"Vorobjev Y. N.","year":"1999","journal-title":"Biophys. Chem."},{"key":"ref46\/cit46","doi-asserted-by":"crossref","first-page":"18680","DOI":"10.1021\/jp063479b","volume":"110","author":"Tan C.","year":"2006","journal-title":"J. Phys. Chem. B"},{"key":"ref47\/cit47","doi-asserted-by":"crossref","first-page":"12263","DOI":"10.1021\/jp073399n","volume":"111","author":"Tan C.","year":"2007","journal-title":"J. Phys. Chem. B"},{"key":"ref48\/cit48","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1016\/0009-2614(93)89366-P","volume":"215","author":"Schlitter J.","year":"1993","journal-title":"Chem. Phys. Lett."},{"key":"ref49\/cit49","doi-asserted-by":"crossref","first-page":"024107","DOI":"10.1063\/1.2746329","volume":"127","author":"Killian B. J.","year":"2007","journal-title":"J. Chem. Phys."},{"key":"ref50\/cit50","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1063\/1.1421362","volume":"116","author":"Hess B.","year":"2002","journal-title":"J. Chem. Phys."},{"key":"ref51\/cit51","doi-asserted-by":"crossref","first-page":"4805","DOI":"10.1021\/ja963641w","volume":"119","author":"Cheatham T. E.","year":"1997","journal-title":"J. Am. Chem. Soc."},{"key":"ref52\/cit52","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"Pettersen E. F.","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref53\/cit53","doi-asserted-by":"crossref","first-page":"6711","DOI":"10.1021\/ja970224q","volume":"119","author":"Zwahlen C.","year":"1997","journal-title":"J. Am. Chem. Soc."},{"key":"ref54\/cit54","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1016\/S0006-3495(97)78756-3","volume":"72","author":"Gilson M. K.","year":"1997","journal-title":"Biophys. J."},{"key":"ref55\/cit55","doi-asserted-by":"crossref","first-page":"2707","DOI":"10.1021\/ja963568+","volume":"119","author":"Hermans J.","year":"1997","journal-title":"J. Am. Chem. Soc."},{"key":"ref56\/cit56","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1002\/prot.10086","volume":"47","author":"Lazaridis T.","year":"2002","journal-title":"Proteins: Struct., Funct., Bioinf."},{"key":"ref57\/cit57","doi-asserted-by":"crossref","first-page":"2934","DOI":"10.1021\/ja994034m","volume":"122","author":"Luo R.","year":"2000","journal-title":"J. Am. Chem. Soc."},{"key":"ref58\/cit58","doi-asserted-by":"crossref","first-page":"1678","DOI":"10.1073\/pnas.68.8.1678","volume":"68","author":"Page M. I.","year":"1971","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"ref59\/cit59","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1016\/S0006-3495(01)75817-1","volume":"81","author":"Yu Y. B.","year":"2001","journal-title":"Biophys. J."},{"key":"ref60\/cit60","doi-asserted-by":"crossref","first-page":"5098","DOI":"10.1021\/ct400383v","volume":"9","author":"Silver N. W.","year":"2013","journal-title":"J. Chem. Theory Comput."},{"key":"ref61\/cit61","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1021\/ct050183l","volume":"2","author":"Geney R.","year":"2006","journal-title":"J. Chem. Theory Comput."},{"key":"ref62\/cit62","doi-asserted-by":"crossref","first-page":"3181","DOI":"10.1021\/ct200384r","volume":"7","author":"Gaillard T.","year":"2011","journal-title":"J. Chem. Theory Comput."},{"key":"ref63\/cit63","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1002\/(SICI)1097-0134(19990101)34:1<69::AID-PROT6>3.0.CO;2-C","volume":"34","author":"Wang J.","year":"1999","journal-title":"Proteins"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/ci500132c","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,5]],"date-time":"2023-04-05T06:43:10Z","timestamp":1680676990000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/ci500132c"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,6,3]]},"references-count":63,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2014,6,23]]}},"alternative-id":["10.1021\/ci500132c"],"URL":"https:\/\/doi.org\/10.1021\/ci500132c","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,6,3]]}}}