{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T22:07:53Z","timestamp":1758924473484},"reference-count":58,"publisher":"American Chemical Society (ACS)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2010,9,27]]},"DOI":"10.1021\/ci100036a","type":"journal-article","created":{"date-parts":[[2010,8,9]],"date-time":"2010-08-09T21:30:12Z","timestamp":1281389412000},"page":"1682-1692","source":"Crossref","is-referenced-by-count":31,"title":["Test MM-PB\/SA on True Conformational Ensembles of Protein\u2212Ligand Complexes"],"prefix":"10.1021","volume":"50","author":[{"given":"Yan","family":"Li","sequence":"first","affiliation":[{"name":"State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, 345 Lingling Road, Shanghai 200032, People\u2019s Republic of China"}]},{"given":"Zhihai","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, 345 Lingling Road, Shanghai 200032, People\u2019s Republic of China"}]},{"given":"Renxiao","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, 345 Lingling Road, Shanghai 200032, People\u2019s Republic of China"}]}],"member":"316","published-online":{"date-parts":[[2010,8,9]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"crossref","first-page":"2395","DOI":"10.1021\/cr00023a004","volume":"93","author":"Kollman P.","year":"1993","journal-title":"Chem. Rev."},{"key":"ref2\/cit2","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1021\/ar00161a004","volume":"22","author":"Jorgensen W. L.","year":"1989","journal-title":"Acc. Chem. Res."},{"key":"ref3\/cit3","first-page":"41","volume-title":"Reviews in Computational Chemistry","author":"B\u00f6hm H. J.","year":"2002"},{"key":"ref4\/cit4","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/j.ddtec.2004.08.004","volume":"1","author":"Schulz-Gasch T.","year":"2004","journal-title":"Drug Discovery Today: Tech."},{"key":"ref5\/cit5","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1021\/ar000033j","volume":"33","author":"Kollman P. A.","year":"2000","journal-title":"Acc. Chem. Res."},{"key":"ref6\/cit6","doi-asserted-by":"crossref","first-page":"3786","DOI":"10.1021\/jm000241h","volume":"43","author":"Kuhn B.","year":"2000","journal-title":"J. Med. Chem."},{"key":"ref7\/cit7","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1002\/(SICI)1097-0134(20000601)39:4<309::AID-PROT40>3.0.CO;2-S","volume":"39","author":"Lee M. R.","year":"2000","journal-title":"Proteins: Struct., Funct., Genet."},{"key":"ref8\/cit8","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1002\/(SICI)1097-0134(20000801)40:2<185::AID-PROT20>3.0.CO;2-X","volume":"40","author":"Kasper P.","year":"2000","journal-title":"Proteins: Struct., Funct., Genet."},{"key":"ref9\/cit9","doi-asserted-by":"crossref","first-page":"1058","DOI":"10.1002\/prot.21044","volume":"64","author":"Xu Y.","year":"2006","journal-title":"Proteins: Struct., Funct., Bioinf."},{"key":"ref10\/cit10","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."},{"key":"ref11\/cit11","doi-asserted-by":"crossref","first-page":"1837","DOI":"10.1021\/jm0505720","volume":"49","author":"Steinbrecher T.","year":"2006","journal-title":"J. Med. Chem."},{"key":"ref12\/cit12","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1021\/ci700041j","volume":"47","author":"Brown S. P.","year":"2007","journal-title":"J. Chem. Inf. Model."},{"key":"ref13\/cit13","doi-asserted-by":"crossref","first-page":"4040","DOI":"10.1021\/jm049081q","volume":"48","author":"Kuhn B.","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref14\/cit14","doi-asserted-by":"crossref","first-page":"7796","DOI":"10.1021\/jm050306m","volume":"48","author":"Pearlman D. A.","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref15\/cit15","doi-asserted-by":"crossref","first-page":"6596","DOI":"10.1021\/jm0608210","volume":"49","author":"Weis A.","year":"2006","journal-title":"J. Med. Chem."},{"key":"ref16\/cit16","doi-asserted-by":"crossref","first-page":"7865","DOI":"10.1016\/j.bmc.2007.08.019","volume":"15","author":"Ferrari A. M.","year":"2007","journal-title":"Bioorg. Chem. Med."},{"key":"ref17\/cit17","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"Berman H. M.","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref18\/cit18","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.pnmrs.2004.08.003","volume":"45","author":"Spronk C.","year":"2004","journal-title":"Prog. Nucl. Magn. Reson. Spectrosc."},{"key":"ref19\/cit19","doi-asserted-by":"crossref","first-page":"2977","DOI":"10.1021\/jm030580l","volume":"47","author":"Wang R.","year":"2004","journal-title":"J. Med. Chem."},{"key":"ref20\/cit20","doi-asserted-by":"crossref","first-page":"4111","DOI":"10.1021\/jm048957q","volume":"48","author":"Wang R.","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref21\/cit21","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1110\/ps.8.3.467","volume":"8","author":"Polshakov V. I.","year":"1999","journal-title":"Protein Sci."},{"key":"ref22\/cit22","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1093\/emboj\/19.7.1505","volume":"19","author":"Zwahlen C.","year":"2000","journal-title":"EMBO J."},{"key":"ref23\/cit23","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1038\/4185","volume":"5","author":"Li S. C.","year":"1998","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref24\/cit24","doi-asserted-by":"crossref","first-page":"5342","DOI":"10.1046\/j.1432-1327.2000.01551.x","volume":"267","author":"Sich C.","year":"2000","journal-title":"Eur. J. Biochem."},{"key":"ref25\/cit25","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1006\/jmbi.2000.4095","volume":"302","author":"Wang P.","year":"2000","journal-title":"J. Mol. Biol."},{"key":"ref26\/cit26","doi-asserted-by":"crossref","first-page":"25456","DOI":"10.1074\/jbc.M102418200","volume":"276","author":"Wang X.","year":"2001","journal-title":"J. Biol. Chem."},{"key":"ref27\/cit27","doi-asserted-by":"crossref","first-page":"31124","DOI":"10.1074\/jbc.M203896200","volume":"277","author":"Wang X.","year":"2002","journal-title":"J. Biol. Chem."},{"key":"ref28\/cit28","doi-asserted-by":"crossref","first-page":"11731","DOI":"10.1021\/bi0262146","volume":"41","author":"Urbaniak M. D.","year":"2002","journal-title":"Biochemistry"},{"key":"ref29\/cit29","doi-asserted-by":"crossref","first-page":"11340","DOI":"10.1074\/jbc.M411579200","volume":"280","author":"Takashima H.","year":"2005","journal-title":"J. Biol. Chem."},{"key":"ref30\/cit30","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1006\/jmbi.2000.5199","volume":"314","author":"Pires J. R.","year":"2001","journal-title":"J. Mol. Biol."},{"key":"ref31\/cit31","doi-asserted-by":"crossref","first-page":"5985","DOI":"10.1093\/emboj\/cdf602","volume":"21","author":"Freund C.","year":"2002","journal-title":"EMBO. J."},{"key":"ref32\/cit32","doi-asserted-by":"crossref","first-page":"48012","DOI":"10.1074\/jbc.M307500200","volume":"278","author":"Cao C.","year":"2003","journal-title":"J. Biol. Chem."},{"key":"ref33\/cit33","doi-asserted-by":"crossref","first-page":"2588","DOI":"10.1110\/ps.03269103","volume":"12","author":"Stevens S. Y.","year":"2003","journal-title":"Protein Sci."},{"key":"ref34\/cit34","doi-asserted-by":"crossref","first-page":"8471","DOI":"10.1074\/jbc.M412318200","volume":"280","author":"Swarbrick J. D.","year":"2005","journal-title":"J. Biol. Chem."},{"key":"ref35\/cit35","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1038\/nsmb1325","volume":"14","author":"Pervushin K.","year":"2007","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref36\/cit36","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1016\/j.molcel.2006.10.026","volume":"24","author":"Taverna S. D.","year":"2006","journal-title":"Mol. Cell"},{"key":"ref37\/cit37","doi-asserted-by":"crossref","first-page":"2454","DOI":"10.1110\/ps.073049407","volume":"16","author":"Runyon S. T.","year":"2007","journal-title":"Protein Sci."},{"key":"ref38\/cit38","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1016\/j.jmb.2007.08.052","volume":"373","author":"Ramirez-Espain X.","year":"2007","journal-title":"J. Mol. Biol."},{"key":"ref39\/cit39","doi-asserted-by":"crossref","first-page":"10864","DOI":"10.1021\/bi700879k","volume":"46","author":"Liu Y.","year":"2007","journal-title":"Biochemistry"},{"key":"ref40\/cit40","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1016\/j.jmb.2007.05.062","volume":"371","author":"Mansy S. S.","year":"2007","journal-title":"J. Mol. Biol."},{"key":"ref41\/cit41","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.AMBER 9;University of California:San Francisco, CA, 2006."},{"key":"ref42\/cit42","unstructured":"Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; and Pople, J. A.Gaussian 03, revision C.02;Gaussian, Inc.:Wallingford, CT, 2004."},{"key":"ref43\/cit43","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":"ref44\/cit44","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1023\/A:1016357811882","volume":"16","author":"Wang R.","year":"2002","journal-title":"J. Comput.-Aided Mol. Des."},{"key":"ref45\/cit45","doi-asserted-by":"crossref","first-page":"6296","DOI":"10.1021\/jm050436v","volume":"48","author":"Velec H. F. G.","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref46\/cit46","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1093\/protein\/8.7.677","volume":"8","author":"Verkhivker G.","year":"1995","journal-title":"Protein Eng."},{"key":"ref47\/cit47","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1023\/A:1008158231558","volume":"14","author":"Verkhivker G. M.","year":"2000","journal-title":"J. Comput.-Aided Mol. Des."},{"key":"ref48\/cit48","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."},{"key":"ref49\/cit49","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1023\/A:1008040323669","volume":"12","author":"Murray C. W.","year":"1998","journal-title":"J. Comput.-Aided Mol. Des."},{"key":"ref50\/cit50","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1021\/ci9000053","volume":"49","author":"Cheng T.","year":"2009","journal-title":"J. Chem. Inf. Model."},{"key":"ref51\/cit51","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1021\/ci8004429","volume":"49","author":"Zhang X.","year":"2009","journal-title":"J. Chem. Inf. Model."},{"key":"ref52\/cit52","unstructured":"Lamm, G.InReviews in Computational Chemistry;Lipkowitz, K. B.; Larter, R.; Cundari, T. R., Eds;John Wiley & Sons Inc.:Hoboken, NJ, 2003; Vol. 19, pp147\u2212365."},{"key":"ref53\/cit53","unstructured":"Baker, N. A.InReviews in Computational Chemistry;Lipkowitz, K. B.; Larter, R.; Cundari, T. R., Eds;John Wiley & Sons Inc.:Hoboken, NJ, 2005; Vol. 21, pp349\u2212379."},{"key":"ref54\/cit54","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1146\/annurev.physchem.51.1.129","volume":"51","author":"Bashford D.","year":"2000","journal-title":"Annu. Rev. Phys. Chem."},{"key":"ref55\/cit55","doi-asserted-by":"crossref","first-page":"6127","DOI":"10.1021\/ja00172a038","volume":"112","author":"Still W. C.","year":"1990","journal-title":"J. Am. Chem. Soc."},{"key":"ref56\/cit56","doi-asserted-by":"crossref","first-page":"5221","DOI":"10.1021\/ja003834q","volume":"123","author":"Wang J.","year":"2001","journal-title":"J. Am. Chem. Soc."},{"key":"ref57\/cit57","doi-asserted-by":"crossref","first-page":"5186","DOI":"10.1016\/j.bmcl.2007.06.095","volume":"17","author":"Xiong Y.","year":"2007","journal-title":"Bioorg. Med. Chem. Lett."},{"key":"ref58\/cit58","doi-asserted-by":"crossref","first-page":"10378","DOI":"10.1073\/pnas.0803847105","volume":"105","author":"Khoruzhii O.","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U.S.A."}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/ci100036a","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,7]],"date-time":"2023-04-07T03:24:17Z","timestamp":1680837857000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/ci100036a"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,8,9]]},"references-count":58,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2010,9,27]]}},"alternative-id":["10.1021\/ci100036a"],"URL":"https:\/\/doi.org\/10.1021\/ci100036a","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,8,9]]}}}