{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T15:39:27Z","timestamp":1782747567250,"version":"3.54.5"},"reference-count":41,"publisher":"American Chemical Society (ACS)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2013,10,28]]},"DOI":"10.1021\/ci400312v","type":"journal-article","created":{"date-parts":[[2013,9,15]],"date-time":"2013-09-15T19:07:42Z","timestamp":1379272062000},"page":"2659-2670","source":"Crossref","is-referenced-by-count":43,"title":["Molecular Recognition in a Diverse Set of Protein\u2013Ligand Interactions Studied with Molecular Dynamics Simulations and End-Point Free Energy Calculations"],"prefix":"10.1021","volume":"53","author":[{"given":"Bo","family":"Wang","sequence":"first","affiliation":[{"name":"Indiana\rUniversity Department of Biochemistry and Molecular Biology, \u2021Center for Computational\rBiology and Bioinformatics, \u00a7Department of Chemistry and Chemical Biology (IUPUI), \u2225Stark Neurosciences\rResearch Institute, Indiana University School of Medicine, 535 Barnhill\rDrive, Indianapolis, Indiana 46202, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liwei","family":"Li","sequence":"additional","affiliation":[{"name":"Indiana\rUniversity Department of Biochemistry and Molecular Biology, \u2021Center for Computational\rBiology and Bioinformatics, \u00a7Department of Chemistry and Chemical Biology (IUPUI), \u2225Stark Neurosciences\rResearch Institute, Indiana University School of Medicine, 535 Barnhill\rDrive, Indianapolis, Indiana 46202, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas D.","family":"Hurley","sequence":"additional","affiliation":[{"name":"Indiana\rUniversity Department of Biochemistry and Molecular Biology, \u2021Center for Computational\rBiology and Bioinformatics, \u00a7Department of Chemistry and Chemical Biology (IUPUI), \u2225Stark Neurosciences\rResearch Institute, Indiana University School of Medicine, 535 Barnhill\rDrive, Indianapolis, Indiana 46202, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samy O.","family":"Meroueh","sequence":"additional","affiliation":[{"name":"Indiana\rUniversity Department of Biochemistry and Molecular Biology, \u2021Center for Computational\rBiology and Bioinformatics, \u00a7Department of Chemistry and Chemical Biology (IUPUI), \u2225Stark Neurosciences\rResearch Institute, Indiana University School of Medicine, 535 Barnhill\rDrive, Indianapolis, Indiana 46202, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2013,10,8]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1021\/ml100031a","volume":"1","author":"Li L.","year":"2010","journal-title":"ACS Med. Chem. Lett."},{"key":"ref2\/cit2","doi-asserted-by":"crossref","first-page":"3686","DOI":"10.1021\/ct200750p","volume":"8","author":"De Ruiter A.","year":"2012","journal-title":"J. Chem. Theory Comput."},{"key":"ref3\/cit3","doi-asserted-by":"crossref","first-page":"2037","DOI":"10.1098\/rsta.2005.1627","volume":"363","author":"Wan S.","year":"2005","journal-title":"Philos. Trans. R. Soc., A"},{"key":"ref4\/cit4","doi-asserted-by":"crossref","first-page":"34665","DOI":"10.1074\/jbc.M313143200","volume":"279","author":"Golemi-Kotra D.","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref5\/cit5","doi-asserted-by":"crossref","first-page":"4594","DOI":"10.1021\/jm001045d","volume":"43","author":"Oostenbrink C. B.","year":"2000","journal-title":"J. Med. Chem."},{"key":"ref6\/cit6","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1007\/s10822-012-9542-5","volume":"26","author":"Lawrenz M.","year":"2012","journal-title":"J. Comput-Aided. Mol. Des."},{"key":"ref7\/cit7","doi-asserted-by":"crossref","first-page":"3446","DOI":"10.1016\/j.bmc.2012.04.019","volume":"20","author":"Steinbrecher T.","year":"2012","journal-title":"Bioorg. Med. Chem."},{"key":"ref8\/cit8","doi-asserted-by":"crossref","first-page":"2523","DOI":"10.1002\/prot.22761","volume":"78","author":"Lawrenz M.","year":"2010","journal-title":"Proteins: Struct., Funct., Bioinf."},{"key":"ref9\/cit9","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1021\/ci3001277","volume":"52","author":"Irwin J. J.","year":"2012","journal-title":"J. Chem. Inf. Model."},{"key":"ref10\/cit10","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1002\/pro.5560070122","volume":"7","author":"Chong L. T.","year":"1998","journal-title":"Protein Sci."},{"key":"ref11\/cit11","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/S0065-3233(03)66002-X","volume":"66","author":"Ponder J. W.","year":"2003","journal-title":"Adv. Protein Chem."},{"key":"ref12\/cit12","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1002\/jcc.10120","volume":"23","author":"Luo R.","year":"2002","journal-title":"J. Comput. Chem."},{"key":"ref13\/cit13","doi-asserted-by":"crossref","first-page":"6127","DOI":"10.1021\/ja00172a038","volume":"112","author":"Still C. W.","year":"1990","journal-title":"J. Am. Chem. Soc."},{"key":"ref14\/cit14","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1021\/ma50003a019","volume":"14","author":"Karplus M.","year":"1981","journal-title":"Macromolecules"},{"key":"ref15\/cit15","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":"ref16\/cit16","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1006\/jmbi.1999.3371","volume":"295","author":"Gohlke H.","year":"2000","journal-title":"J. Mol. Biol."},{"key":"ref17\/cit17","doi-asserted-by":"crossref","first-page":"12766","DOI":"10.1021\/ja060830y","volume":"128","author":"Basdevant N.","year":"2006","journal-title":"J. Am. Chem. Soc."},{"key":"ref18\/cit18","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1016\/j.str.2006.01.014","volume":"14","author":"Gr\u00fcnberg R.","year":"2006","journal-title":"Structure"},{"key":"ref19\/cit19","doi-asserted-by":"crossref","first-page":"2680","DOI":"10.1021\/ci200191m","volume":"51","author":"Lill M. A.","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"ref20\/cit20","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1111\/j.1747-0285.2008.00661.x","volume":"71","author":"Li L.","year":"2008","journal-title":"Chem. Biol. Drug Des."},{"key":"ref21\/cit21","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1021\/ci100490w","volume":"51","author":"Li L.","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"ref22\/cit22","doi-asserted-by":"crossref","first-page":"2132","DOI":"10.1021\/ci200078f","volume":"51","author":"Li L.","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"ref23\/cit23","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1006\/jmbi.1998.2401","volume":"285","author":"Word J. M.","year":"1999","journal-title":"J. Mol. Biol."},{"key":"ref24\/cit24","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":"ref25\/cit25","volume-title":"AMBER9","author":"Case D. A.","year":"2006"},{"key":"ref26\/cit26","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":"ref27\/cit27","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1002\/jcc.10349","volume":"24","author":"Duan Y.","year":"2003","journal-title":"J. Comput. Chem."},{"key":"ref28\/cit28","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":"ref29\/cit29","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":"ref30\/cit30","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1023\/A:1008763014207","volume":"18","author":"Massova I.","year":"2000","journal-title":"Perspect. Drug Discovery Des."},{"key":"ref31\/cit31","doi-asserted-by":"crossref","first-page":"3986","DOI":"10.1021\/ja003164o","volume":"123","author":"Wang W.","year":"2001","journal-title":"J. Am. Chem. Soc."},{"key":"ref32\/cit32","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1126\/science.7761829","volume":"268","author":"Honig B.","year":"1995","journal-title":"Science"},{"key":"ref33\/cit33","doi-asserted-by":"crossref","first-page":"1978","DOI":"10.1021\/j100058a043","volume":"98","author":"Sitkoff D.","year":"1994","journal-title":"J. Phys. Chem."},{"key":"ref34\/cit34","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1107\/S0021889883010985","volume":"16","author":"Connolly M. L.","year":"1983","journal-title":"J. Appl. Crystallogr."},{"key":"ref35\/cit35","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":"ref36\/cit36","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."},{"key":"ref37\/cit37","doi-asserted-by":"crossref","first-page":"3712","DOI":"10.1021\/jp994072s","volume":"104","author":"Onufriev A.","year":"2000","journal-title":"J. Phys. Chem. B"},{"key":"ref38\/cit38","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1021\/bi8017043","volume":"48","author":"Liang S.","year":"2008","journal-title":"Biochemistry"},{"key":"ref39\/cit39","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1007\/s10822-008-9196-5","volume":"22","author":"Jain A.","year":"2008","journal-title":"J. Comput.-Aided Mol. Des."},{"key":"ref40\/cit40","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1093\/protein\/gzp042","volume":"22","author":"Li L.","year":"2009","journal-title":"Protein Eng., Des. Sel."},{"key":"ref41\/cit41","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1002\/prot.340200108","volume":"20","author":"Lee K. H.","year":"1994","journal-title":"Proteins: Struct., Funct., Bioinf."}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/ci400312v","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,2]],"date-time":"2023-04-02T21:08:16Z","timestamp":1680469696000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/ci400312v"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,10,8]]},"references-count":41,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2013,10,28]]}},"alternative-id":["10.1021\/ci400312v"],"URL":"https:\/\/doi.org\/10.1021\/ci400312v","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,10,8]]}}}