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Res."},{"key":"ref4\/cit4","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1146\/annurev.bb.18.060189.002243","volume":"18","author":"Beveridge D. L.","year":"1989","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"issue":"3","key":"ref5\/cit5","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1093\/protein\/7.3.385","volume":"7","author":"Aqvist J.","year":"1994","journal-title":"Protein Eng."},{"issue":"5","key":"ref6\/cit6","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1023\/A:1007996124545","volume":"11","author":"Eldridge M. D.","year":"1997","journal-title":"J. Comput.-Aided Mol. Des."},{"issue":"3","key":"ref7\/cit7","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/BF00126743","volume":"8","author":"Bohm H. J.","year":"1994","journal-title":"J. Comput.-Aided Mol. Des."},{"issue":"12","key":"ref8\/cit8","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1007\/s008940050096","volume":"4","author":"Wang R. 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Biol."},{"issue":"4","key":"ref13\/cit13","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1016\/j.jmb.2007.12.054","volume":"376","author":"Hou T. J.","year":"2008","journal-title":"J. Mol. Biol."},{"issue":"4","key":"ref14\/cit14","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1074\/mcp.M800450-MCP200","volume":"8","author":"Hou T. J.","year":"2009","journal-title":"Mol. Cell Proteomics"},{"issue":"21","key":"ref15\/cit15","doi-asserted-by":"crossref","first-page":"5527","DOI":"10.1021\/jp015516z","volume":"106","author":"Hou T. J.","year":"2002","journal-title":"J. Phys. Chem. B"},{"issue":"26","key":"ref16\/cit16","doi-asserted-by":"crossref","first-page":"14937","DOI":"10.1073\/pnas.251265598","volume":"98","author":"Wang W.","year":"2001","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"issue":"2","key":"ref17\/cit17","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1002\/prot.20192","volume":"57","author":"Lepsik M.","year":"2004","journal-title":"Proteins: Struct. Funct. Bioinf."},{"issue":"20","key":"ref18\/cit18","doi-asserted-by":"crossref","first-page":"3786","DOI":"10.1021\/jm000241h","volume":"43","author":"Kuhn B.","year":"2000","journal-title":"J. Med. Chem."},{"issue":"7","key":"ref19\/cit19","doi-asserted-by":"crossref","first-page":"1412","DOI":"10.1021\/jm010338j","volume":"45","author":"Huo S. H.","year":"2002","journal-title":"J. Med. Chem."},{"issue":"3","key":"ref20\/cit20","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1021\/ci050488t","volume":"46","author":"Brown S. P.","year":"2006","journal-title":"J. Chem. Inf. Model."},{"issue":"8","key":"ref21\/cit21","doi-asserted-by":"crossref","first-page":"2639","DOI":"10.1021\/ja0779250","volume":"130","author":"Stoica I.","year":"2008","journal-title":"J. Am. Chem. Soc."},{"issue":"1","key":"ref22\/cit22","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1021\/ci025552a","volume":"43","author":"Hou T. J.","year":"2003","journal-title":"J. Chem. Inf. Comput. Sci."},{"issue":"6","key":"ref23\/cit23","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1021\/jm0609162","volume":"50","author":"Hou T. J.","year":"2007","journal-title":"J. Med. Chem."},{"issue":"4","key":"ref24\/cit24","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4057","volume":"303","author":"Wang W.","year":"2000","journal-title":"J. Mol. Biol."},{"issue":"1","key":"ref25\/cit25","first-page":"46","volume":"2","author":"Hou T. J.","year":"2006","journal-title":"Plos Comput. Biol."},{"issue":"2","key":"ref26\/cit26","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1002\/jcc.10379","volume":"25","author":"Gohlke H.","year":"2004","journal-title":"J. Comput. Chem."},{"issue":"24","key":"ref27\/cit27","doi-asserted-by":"crossref","first-page":"7796","DOI":"10.1021\/jm050306m","volume":"48","author":"Pearlman D. A.","year":"2005","journal-title":"J. Med. Chem."},{"issue":"12","key":"ref28\/cit28","doi-asserted-by":"crossref","first-page":"4040","DOI":"10.1021\/jm049081q","volume":"48","author":"Kuhn B.","year":"2005","journal-title":"J. Med. Chem."},{"issue":"22","key":"ref29\/cit29","doi-asserted-by":"crossref","first-page":"6596","DOI":"10.1021\/jm0608210","volume":"49","author":"Weis A.","year":"2006","journal-title":"J. Med. Chem."},{"issue":"3","key":"ref30\/cit30","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1002\/prot.340160303","volume":"16","author":"Miyamoto S.","year":"1993","journal-title":"Proteins: Struct. Funct. Bioinf."},{"issue":"10","key":"ref31\/cit31","doi-asserted-by":"crossref","first-page":"1242","DOI":"10.1002\/jcc.20047","volume":"25","author":"Almlof M.","year":"2004","journal-title":"J. Comput. Chem."},{"issue":"1","key":"ref32\/cit32","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"},{"issue":"3","key":"ref33\/cit33","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1006\/jmbi.1993.1321","volume":"231","author":"Pugliese L.","year":"1993","journal-title":"J. Mol. Biol."},{"issue":"3","key":"ref34\/cit34","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1042\/bj1010774","volume":"101","author":"Green N. M.","year":"1966","journal-title":"Biochem. J."},{"issue":"3","key":"ref35\/cit35","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1016\/0022-2836(87)90190-2","volume":"195","author":"Poulos T. L.","year":"1987","journal-title":"J. Mol. Biol."},{"key":"ref36\/cit36","unstructured":"SYBYL molecular simulation package.http:\/\/www.sybyl.com(accessed Nov 2010)."},{"issue":"40","key":"ref37\/cit37","doi-asserted-by":"crossref","first-page":"10269","DOI":"10.1021\/j100142a004","volume":"97","author":"Bayly C. I.","year":"1993","journal-title":"J. Phys. Chem."},{"issue":"6","key":"ref38\/cit38","doi-asserted-by":"crossref","first-page":"1546","DOI":"10.1021\/ci050151r","volume":"45","author":"Bren U.","year":"2005","journal-title":"J. Chem. Inf. Model."},{"key":"ref39\/cit39","volume-title":"Gaussian 03","author":"Frisch M. J.","year":"2004"},{"issue":"2","key":"ref40\/cit40","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.jmgm.2005.12.005","volume":"25","author":"Wang J. M.","year":"2006","journal-title":"J. Mol. Graphics Model."},{"issue":"16","key":"ref41\/cit41","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1002\/jcc.10349","volume":"24","author":"Duan Y.","year":"2003","journal-title":"J. Comput. Chem."},{"issue":"9","key":"ref42\/cit42","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1002\/jcc.20035","volume":"25","author":"Wang J. M.","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref43\/cit43","unstructured":"Giammona, D. A.An examination of conformational flexibility in porphyrin and bulky-ligand binding in myoglobin.Ph.D. thesis,University of California at Davis, 1984."},{"issue":"12","key":"ref44\/cit44","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"Darden T.","year":"1993","journal-title":"J. Chem. Phys."},{"key":"ref45\/cit45","doi-asserted-by":"crossref","first-page":"2384","DOI":"10.1063\/1.439486","volume":"72","author":"Andersen H. C.","year":"1980","journal-title":"J. Chem. Phys."},{"issue":"16","key":"ref46\/cit46","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."},{"issue":"3","key":"ref47\/cit47","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."},{"issue":"28","key":"ref48\/cit48","doi-asserted-by":"crossref","first-page":"6507","DOI":"10.1021\/jp010454y","volume":"105","author":"Rocchia W.","year":"2001","journal-title":"J. Phys. Chem. B"},{"issue":"7","key":"ref49\/cit49","doi-asserted-by":"crossref","first-page":"1978","DOI":"10.1021\/j100058a043","volume":"98","author":"Sitkoff D.","year":"1994","journal-title":"J. Phys. Chem."},{"issue":"9","key":"ref50\/cit50","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1023\/A:1011625728803","volume":"37","author":"Batsanov S. S.","year":"2001","journal-title":"Inorg. Mater."},{"issue":"2","key":"ref51\/cit51","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1002\/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A","volume":"20","author":"Weiser J.","year":"1999","journal-title":"J. Comput. Chem."},{"issue":"1","key":"ref52\/cit52","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."},{"issue":"51","key":"ref53\/cit53","doi-asserted-by":"crossref","first-page":"19824","DOI":"10.1021\/jp961710n","volume":"100","author":"Hawkins G. D.","year":"1996","journal-title":"J. Phys. Chem."},{"issue":"4","key":"ref54\/cit54","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1002\/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E","volume":"56","author":"Tsui V.","year":"2000","journal-title":"Biopolymers"},{"issue":"2","key":"ref55\/cit55","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1002\/prot.20033","volume":"55","author":"Onufriev A.","year":"2004","journal-title":"Proteins: Struct. Funct. Bioinf."},{"issue":"10","key":"ref56\/cit56","doi-asserted-by":"crossref","first-page":"2323","DOI":"10.1021\/ci900277r","volume":"49","author":"Udommaneethanakit T.","year":"2009","journal-title":"J. Chem. Inf. Model."},{"issue":"10","key":"ref57\/cit57","doi-asserted-by":"crossref","first-page":"4691","DOI":"10.1073\/pnas.92.10.4691","volume":"92","author":"Misra V. K.","year":"1995","journal-title":"Proc. Natl. Acad. Sci. 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