{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T08:51:20Z","timestamp":1762505480088},"reference-count":39,"publisher":"American Chemical Society (ACS)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2009,7,27]]},"DOI":"10.1021\/ci900012k","type":"journal-article","created":{"date-parts":[[2009,6,18]],"date-time":"2009-06-18T17:56:33Z","timestamp":1245347793000},"page":"1751-1761","source":"Crossref","is-referenced-by-count":26,"title":["Molecular Dynamics and Free Energy Studies on the Wild-Type and Mutated HIV-1 Protease Complexed with Four Approved Drugs: Mechanism of Binding and Drug Resistance"],"prefix":"10.1021","volume":"49","author":[{"given":"Stefano","family":"Alcaro","sequence":"first","affiliation":[{"name":"Laboratorio di Chimica Farmaceutica Computazionale - Dipartimento di Scienze Farmacobiologiche, Universit\u00e0 \u201cMagna Gr\u00e6cia\u201d di Catanzaro, Campus Universitario, Viale Europa, 88100 Catanzaro, Italy, Dipartimento di Medicina Sperimentale e Biochimica, Universit\u00e0 \u201cTor Vergata\u201d, Via Montpellier, 1, 00133, Roma, Italy, and Max-Planck-Institute for Informatics, Saarbr\u00fccken, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Artese","sequence":"additional","affiliation":[{"name":"Laboratorio di Chimica Farmaceutica Computazionale - Dipartimento di Scienze Farmacobiologiche, Universit\u00e0 \u201cMagna Gr\u00e6cia\u201d di Catanzaro, Campus Universitario, Viale Europa, 88100 Catanzaro, Italy, Dipartimento di Medicina Sperimentale e Biochimica, Universit\u00e0 \u201cTor Vergata\u201d, Via Montpellier, 1, 00133, Roma, Italy, and Max-Planck-Institute for Informatics, Saarbr\u00fccken, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesca","family":"Ceccherini-Silberstein","sequence":"additional","affiliation":[{"name":"Laboratorio di Chimica Farmaceutica Computazionale - Dipartimento di Scienze Farmacobiologiche, Universit\u00e0 \u201cMagna Gr\u00e6cia\u201d di Catanzaro, Campus Universitario, Viale Europa, 88100 Catanzaro, Italy, Dipartimento di Medicina Sperimentale e Biochimica, Universit\u00e0 \u201cTor Vergata\u201d, Via Montpellier, 1, 00133, Roma, Italy, and Max-Planck-Institute for Informatics, Saarbr\u00fccken, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesco","family":"Ortuso","sequence":"additional","affiliation":[{"name":"Laboratorio di Chimica Farmaceutica Computazionale - Dipartimento di Scienze Farmacobiologiche, Universit\u00e0 \u201cMagna Gr\u00e6cia\u201d di Catanzaro, Campus Universitario, Viale Europa, 88100 Catanzaro, Italy, Dipartimento di Medicina Sperimentale e Biochimica, Universit\u00e0 \u201cTor Vergata\u201d, Via Montpellier, 1, 00133, Roma, Italy, and Max-Planck-Institute for Informatics, Saarbr\u00fccken, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlo Federico","family":"Perno","sequence":"additional","affiliation":[{"name":"Laboratorio di Chimica Farmaceutica Computazionale - Dipartimento di Scienze Farmacobiologiche, Universit\u00e0 \u201cMagna Gr\u00e6cia\u201d di Catanzaro, Campus Universitario, Viale Europa, 88100 Catanzaro, Italy, Dipartimento di Medicina Sperimentale e Biochimica, Universit\u00e0 \u201cTor Vergata\u201d, Via Montpellier, 1, 00133, Roma, Italy, and Max-Planck-Institute for Informatics, Saarbr\u00fccken, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tobias","family":"Sing","sequence":"additional","affiliation":[{"name":"Laboratorio di Chimica Farmaceutica Computazionale - Dipartimento di Scienze Farmacobiologiche, Universit\u00e0 \u201cMagna Gr\u00e6cia\u201d di Catanzaro, Campus Universitario, Viale Europa, 88100 Catanzaro, Italy, Dipartimento di Medicina Sperimentale e Biochimica, Universit\u00e0 \u201cTor Vergata\u201d, Via Montpellier, 1, 00133, Roma, Italy, and Max-Planck-Institute for Informatics, Saarbr\u00fccken, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valentina","family":"Svicher","sequence":"additional","affiliation":[{"name":"Laboratorio di Chimica Farmaceutica Computazionale - Dipartimento di Scienze Farmacobiologiche, Universit\u00e0 \u201cMagna Gr\u00e6cia\u201d di Catanzaro, Campus Universitario, Viale Europa, 88100 Catanzaro, Italy, Dipartimento di Medicina Sperimentale e Biochimica, Universit\u00e0 \u201cTor Vergata\u201d, Via Montpellier, 1, 00133, Roma, Italy, and Max-Planck-Institute for Informatics, Saarbr\u00fccken, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"316","published-online":{"date-parts":[[2009,6,18]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1146\/annurev.med.53.052901.131947","volume":"53","author":"Wlodawer A.","year":"2002","journal-title":"Annu. Rev. Med."},{"key":"ref2\/cit2","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1038\/337576a0","volume":"337","author":"Miller M.","year":"1989","journal-title":"Nature"},{"key":"ref3\/cit3","doi-asserted-by":"crossref","first-page":"4663","DOI":"10.1021\/bi00233a005","volume":"30","author":"Rao J. K. M.","year":"1991","journal-title":"Biochemistry"},{"key":"ref4\/cit4","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1146\/annurev.bb.19.060190.001201","volume":"19","author":"Davies D. R.","year":"1990","journal-title":"Annu. Rev. Biophys. Biophys. Chem."},{"key":"ref5\/cit5","unstructured":"Protein Data Bank.http:\/\/www.rcsb.org\/PDB(accessed February 2009)."},{"key":"ref6\/cit6","first-page":"6","volume":"9","author":"Tomasselli A. G.","year":"1991","journal-title":"Chim. Oggi"},{"key":"ref7\/cit7","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1146\/annurev.bi.62.070193.002551","volume":"62","author":"Wlodawer A.","year":"1993","journal-title":"Annu. Rev. Biochem."},{"key":"ref8\/cit8","doi-asserted-by":"crossref","first-page":"2015","DOI":"10.1128\/AAC.49.5.2015-2025.2005","volume":"49","author":"Svicher V.","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref9\/cit9","first-page":"83","volume":"3","author":"Hertogs K.","year":"1999","journal-title":"Recent Res. Dev. Antimicrob. Agents Chemother."},{"key":"ref10\/cit10","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1111\/j.0966-0410.2004.00479.x","volume":"12","author":"Johnson V. A.","year":"2004","journal-title":"Top. HIV Med."},{"key":"ref11\/cit11","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1086\/589297","volume":"47","author":"Hirsch M. S.","year":"2008","journal-title":"Clin. Infect. Dis."},{"key":"ref12\/cit12","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1097\/QAD.0b013e3282f51eb9","volume":"22","author":"Poveda E.","year":"2008","journal-title":"AIDS"},{"key":"ref13\/cit13","doi-asserted-by":"crossref","first-page":"3943","DOI":"10.1093\/bioinformatics\/bti654","volume":"21","author":"Beerenwinkel N.","year":"2005","journal-title":"Bioinformatics"},{"key":"ref14\/cit14","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1021\/jm0609162","volume":"50","author":"Hou T.","year":"2007","journal-title":"J. Med. Chem."},{"key":"ref15\/cit15","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1093\/jac\/dkg392","volume":"52","author":"Paulsen D.","year":"2003","journal-title":"J. Antimicrob. Chemother."},{"key":"ref16\/cit16","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.jmb.2008.05.062","volume":"381","author":"Liu F.","year":"2008","journal-title":"J. Mol. Biol."},{"issue":"2","key":"ref17\/cit17","first-page":"27","volume":"9","author":"Roberts N. A.","year":"1995","journal-title":"AIDS"},{"key":"ref18\/cit18","doi-asserted-by":"crossref","first-page":"3816","DOI":"10.1128\/AAC.49.9.3816-3824.2005","volume":"49","author":"Weinheimer S.","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref19\/cit19","doi-asserted-by":"crossref","first-page":"2803","DOI":"10.1016\/S0968-0896(02)00051-2","volume":"10","author":"Stoll V.","year":"2002","journal-title":"Bioorg. Med. Chem."},{"key":"ref20\/cit20","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1021\/jm049560p","volume":"48","author":"Surleraux D. L. N. G.","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref21\/cit21","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1002\/prot.21304","volume":"67","author":"Tie Y.","year":"2007","journal-title":"Proteins"},{"key":"ref22\/cit22","doi-asserted-by":"crossref","first-page":"5144","DOI":"10.1128\/JVI.02706-06","volume":"81","author":"Armstrong A. A.","year":"2007","journal-title":"J. Virol."},{"key":"ref23\/cit23","doi-asserted-by":"crossref","first-page":"4805","DOI":"10.1021\/jm060522a","volume":"49","author":"Lyne P. D.","year":"2006","journal-title":"J. Med. Chem."},{"key":"ref24\/cit24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0166-1280(96)04869-5","volume":"423","author":"Weber I. T.","year":"1998","journal-title":"J. Mol. Struct."},{"key":"ref25\/cit25","doi-asserted-by":"crossref","first-page":"13459","DOI":"10.1074\/jbc.M708506200","volume":"283","author":"Sayer J. M.","year":"2008","journal-title":"J. Biol. Chem."},{"key":"ref26\/cit26","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1097\/QAD.0b013e328011e691","volume":"21","author":"Shafer R. W.","year":"2007","journal-title":"AIDS"},{"key":"ref27\/cit27","doi-asserted-by":"crossref","first-page":"14865","DOI":"10.1021\/bi700864p","volume":"46","author":"Sadiq S. K.","year":"2007","journal-title":"Biochemistry"},{"key":"ref28\/cit28","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1016\/j.jmb.2006.02.076","volume":"358","author":"Liu F.","year":"2006","journal-title":"J. Mol. Biol."},{"key":"ref29\/cit29","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.jmb.2006.08.007","volume":"363","author":"Kovalevsky A. Y.","year":"2006","journal-title":"J. Mol. Biol."},{"key":"ref30\/cit30","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/j.jmb.2005.09.095","volume":"354","author":"Liu F.","year":"2005","journal-title":"J. Mol. Biol."},{"key":"ref31\/cit31","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1006\/jmbi.2001.5173","volume":"315","author":"Zoete V.","year":"2002","journal-title":"J. Mol. Biol."},{"key":"ref32\/cit32","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1110\/ps.03468904","volume":"13","author":"Perryman A. L.","year":"2004","journal-title":"Protein Sci."},{"key":"ref33\/cit33","unstructured":"Stanford Database.http:\/\/hivdb.Stanford.edu(accessed February 2009)."},{"key":"ref34\/cit34","unstructured":"geno2pheno Web-based prediction service.http:\/\/www.geno2pheno.org(accessed February 2009)."},{"key":"ref35\/cit35","doi-asserted-by":"crossref","first-page":"7743","DOI":"10.1016\/0040-4039(93)88034-G","volume":"33","author":"McDonald D. Q.","year":"1992","journal-title":"Tetrahedron Lett."},{"key":"ref36\/cit36","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":"ref37\/cit37","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1002\/jcc.540110405","volume":"11","author":"Mohamadi F.","year":"1990","journal-title":"J. Comput. Chem."},{"key":"ref38\/cit38","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1002\/(SICI)1096-987X(200005)21:7<515::AID-JCC2>3.0.CO;2-5","volume":"21","author":"Alcaro S.","year":"2000","journal-title":"J. Comput. Chem."},{"key":"ref39\/cit39","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/protein\/8.2.127","volume":"8","author":"Wallace A. C.","year":"1995","journal-title":"Protein Eng."}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/ci900012k","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,4]],"date-time":"2023-04-04T13:23:25Z","timestamp":1680614605000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/ci900012k"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,6,18]]},"references-count":39,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2009,7,27]]}},"alternative-id":["10.1021\/ci900012k"],"URL":"https:\/\/doi.org\/10.1021\/ci900012k","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,6,18]]}}}