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Biol."},{"key":"ref11\/cit11","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1021\/bi051887k","volume":"45","author":"Salter J.","year":"2006","journal-title":"Biochemistry"},{"key":"ref12\/cit12","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1021\/ct0503015","volume":"2","author":"Park H.","year":"2006","journal-title":"J. Chem. Theory Comput."},{"key":"ref13\/cit13","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1016\/j.molcel.2007.12.001","volume":"28","author":"Walter N. G.","year":"2007","journal-title":"Mol. Cell"},{"key":"ref14\/cit14","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1021\/ar800050c","volume":"41","author":"Cochrane J. C.","year":"2008","journal-title":"Acc. Chem. Res."},{"key":"ref15\/cit15","doi-asserted-by":"crossref","first-page":"6434","DOI":"10.1093\/emboj\/20.22.6434","volume":"20","author":"Pinard R.","year":"2001","journal-title":"EMBO J."},{"key":"ref16\/cit16","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.jmb.2004.04.067","volume":"340","author":"Kuzmin Y. I.","year":"2004","journal-title":"J. Mol. Biol."},{"key":"ref17\/cit17","doi-asserted-by":"crossref","first-page":"7088","DOI":"10.1093\/nar\/gkn871","volume":"36","author":"Ditzler M. A.","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"ref18\/cit18","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1038\/35071009","volume":"410","author":"Rupert P. B.","year":"2001","journal-title":"Nature"},{"key":"ref19\/cit19","doi-asserted-by":"crossref","first-page":"1421","DOI":"10.1126\/science.1076093","volume":"298","author":"Rupert P. 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T.","year":"2007","journal-title":"RNA"},{"key":"ref29\/cit29","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1261\/rna.1055308","volume":"14","author":"Macelrevey C.","year":"2008","journal-title":"RNA"},{"key":"ref30\/cit30","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1016\/j.bbrc.2008.04.036","volume":"371","author":"Torelli A. T.","year":"2008","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref31\/cit31","doi-asserted-by":"crossref","first-page":"6093","DOI":"10.1021\/ja900450h","volume":"131","author":"Spitale R. C.","year":"2009","journal-title":"J. Am. Chem. Soc."},{"key":"ref32\/cit32","doi-asserted-by":"crossref","first-page":"12908","DOI":"10.1021\/ja9060883","volume":"131","author":"Guo M.","year":"2009","journal-title":"J. Am. Chem. Soc."},{"key":"ref33\/cit33","unstructured":"Case, D. A.; Darden, T. A.; Cheatham, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Pearlman, D. A.; Crowley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Mathews, D. H.; Schafmeister, C.; Ross, W. S.; Kollman, P. A.University of California:San Francisco, 2006."},{"key":"ref34\/cit34","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1002\/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F","volume":"21","author":"Wang J. M.","year":"2000","journal-title":"J. Comput. Chem."},{"key":"ref35\/cit35","doi-asserted-by":"crossref","first-page":"3817","DOI":"10.1529\/biophysj.106.097782","volume":"92","author":"Perez A.","year":"2007","journal-title":"Biophys. J."},{"key":"ref36\/cit36","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":"ref37\/cit37","doi-asserted-by":"crossref","first-page":"5179","DOI":"10.1021\/ja00124a002","volume":"117","author":"Cornell W. D.","year":"1995","journal-title":"J. Am. Chem. Soc."},{"key":"ref38\/cit38","doi-asserted-by":"crossref","first-page":"9620","DOI":"10.1021\/ja00074a030","volume":"115","author":"Cornell W. D.","year":"1993","journal-title":"J. Am. Chem. Soc."},{"key":"ref39\/cit39","volume-title":"Gaussian 03","author":"Frisch M. J.","year":"2003"},{"key":"ref40\/cit40","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1021\/ar900093g","volume":"43","author":"Ditzler M. A.","year":"2010","journal-title":"Acc. Chem. Res."},{"key":"ref41\/cit41","doi-asserted-by":"crossref","first-page":"4898","DOI":"10.1093\/nar\/gkp468","volume":"37","author":"Zirbel C. L.","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref42\/cit42","doi-asserted-by":"crossref","first-page":"2379","DOI":"10.1093\/nar\/gkn082","volume":"36","author":"Perez A.","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"ref43\/cit43","doi-asserted-by":"crossref","first-page":"14739","DOI":"10.1021\/ja0753546","volume":"129","author":"Perez A.","year":"2007","journal-title":"J. Am. Chem. Soc."},{"key":"ref44\/cit44","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1002\/bip.20620","volume":"85","author":"McDowell S. E.","year":"2007","journal-title":"Biopolymers"},{"key":"ref45\/cit45","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.ymeth.2007.02.004","volume":"43","author":"Sponer J.","year":"2007","journal-title":"Methods"},{"key":"ref46\/cit46","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1093\/nar\/gkj470","volume":"34","author":"Spackova N.","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref47\/cit47","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1002\/bip.20503","volume":"82","author":"Reblova K.","year":"2006","journal-title":"Biopolymers"},{"key":"ref48\/cit48","doi-asserted-by":"crossref","first-page":"10701","DOI":"10.1039\/b911169g","volume":"11","author":"Besseova I.","year":"2009","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref49\/cit49","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1529\/biophysj.103.034751","volume":"87","author":"Fadrna E.","year":"2004","journal-title":"Biophys. J."},{"key":"ref50\/cit50","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.ymeth.2009.04.007","volume":"49","author":"Banas P.","year":"2009","journal-title":"Methods"},{"key":"ref51\/cit51","doi-asserted-by":"crossref","first-page":"2514","DOI":"10.1021\/ct900200k","volume":"5","author":"Fadrna E.","year":"2009","journal-title":"J. Chem. Theory Comput."},{"key":"ref52\/cit52","doi-asserted-by":"crossref","first-page":"3932","DOI":"10.1529\/biophysj.107.110056","volume":"93","author":"Reblova K.","year":"2007","journal-title":"Biophys. J."},{"key":"ref53\/cit53","doi-asserted-by":"crossref","first-page":"11177","DOI":"10.1021\/jp802592z","volume":"112","author":"Banas P.","year":"2008","journal-title":"J. Phys. Chem. B"},{"key":"ref54\/cit54","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.1093\/nar\/30.6.1287","volume":"30","author":"Ryder S. P.","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref55\/cit55","doi-asserted-by":"crossref","first-page":"14396","DOI":"10.1021\/bi051550i","volume":"44","author":"Alam S.","year":"2005","journal-title":"Biochemistry"},{"key":"ref56\/cit56","doi-asserted-by":"crossref","first-page":"6026","DOI":"10.1021\/bi952985g","volume":"35","author":"Cai Z. P.","year":"1996","journal-title":"Biochemistry"},{"key":"ref57\/cit57","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1038\/6651","volume":"6","author":"Butcher S. E.","year":"1999","journal-title":"Nat. Struct. Biol."},{"key":"ref58\/cit58","doi-asserted-by":"crossref","first-page":"3723","DOI":"10.1021\/bi0028385","volume":"40","author":"Hampel K. 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