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Rev."},{"issue":"13","key":"ref50\/cit50","doi-asserted-by":"crossref","first-page":"3313","DOI":"10.1021\/bi00064a014","volume":"32","author":"Goodin D. B.","year":"1993","journal-title":"Biochem. J."},{"issue":"2","key":"ref51\/cit51","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1042\/bj0540347","volume":"54","author":"Green N. M.","year":"1953","journal-title":"Biochem. J."},{"key":"ref52\/cit52","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1038\/nsb1094-735","volume":"1","author":"Kurinov I.","year":"1994","journal-title":"Nat. Struct. Biol."},{"key":"ref53\/cit53","doi-asserted-by":"crossref","first-page":"6903","DOI":"10.1021\/jp001177i","volume":"104","author":"Banba S.","year":"2000","journal-title":"J. Phys. Chem."},{"key":"ref54\/cit54","doi-asserted-by":"crossref","first-page":"3423","DOI":"10.1063\/1.1287147","volume":"113","author":"Banba S.","year":"2000","journal-title":"J. Chem. Phys."},{"issue":"8","key":"ref55\/cit55","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1023\/B:JCAM.0000004604.87558.02","volume":"17","author":"Rosenfeld R. J.","year":"2003","journal-title":"J. Comput.-Aided Mol. Des."},{"issue":"10","key":"ref56\/cit56","doi-asserted-by":"crossref","first-page":"2010","DOI":"10.1021\/ci800154w","volume":"48","author":"Deng W.","year":"2008","journal-title":"J. Chem. Inf. Model."},{"key":"ref57\/cit57","unstructured":"Warshel, A.Computer Modeling of Chemical Reactions in Enzymes;Wiley:New York, 1991; pp1\u2212256."},{"key":"ref58\/cit58","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1002\/9780470125847.ch3","volume-title":"Reviews in Computational Chemistry","volume":"7","author":"Gao J.","year":"1995"},{"key":"ref59\/cit59","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1146\/annurev.physchem.59.032607.093618","volume":"59","author":"Hu H.","year":"2007","journal-title":"Annu. Rev. Phys. 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