{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T04:36:08Z","timestamp":1781930168497,"version":"3.54.5"},"reference-count":67,"publisher":"American Chemical Society (ACS)","issue":"7","funder":[{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","award":["FP7\/2007\/2013 N\u00b0238013"],"award-info":[{"award-number":["FP7\/2007\/2013 N\u00b0238013"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2014,7,28]]},"DOI":"10.1021\/ci500164q","type":"journal-article","created":{"date-parts":[[2014,7,8]],"date-time":"2014-07-08T19:08:03Z","timestamp":1404846483000},"page":"2093-2104","source":"Crossref","is-referenced-by-count":23,"title":["Free Energy Predictions of Ligand Binding to an \u03b1-Helix Using Steered Molecular Dynamics and Umbrella Sampling Simulations"],"prefix":"10.1021","volume":"54","author":[{"given":"Jan K.","family":"Marzinek","sequence":"first","affiliation":[{"name":"National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543"},{"name":"Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, Singapore 138671"},{"name":"Unilever R&D, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, United Kingdom"},{"name":"Department of Chemical Engineering and Chemical Technology, Imperial College London, London, SW7 2BY, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter J.","family":"Bond","sequence":"additional","affiliation":[{"name":"National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543"},{"name":"Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, Singapore 138671"},{"name":"The Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guoping","family":"Lian","sequence":"additional","affiliation":[{"name":"Unilever R&D, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, United Kingdom"},{"name":"Department of Chemical and Process Engineering, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanyan","family":"Zhao","sequence":"additional","affiliation":[{"name":"China Agricultural University, Beijing 100083, People\u2019s Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lujia","family":"Han","sequence":"additional","affiliation":[{"name":"China Agricultural University, Beijing 100083, People\u2019s Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Massimo G.","family":"Noro","sequence":"additional","affiliation":[{"name":"Physical and Chemical Insights Group, Unilever R&D, Port Sunlight, Wirral, CH63 3JW, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Efstratios N.","family":"Pistikopoulos","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering and Chemical Technology, Imperial College London, London, SW7 2BY, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Athanasios","family":"Mantalaris","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering and Chemical Technology, Imperial College London, London, SW7 2BY, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2014,7,17]]},"reference":[{"key":"ref1\/cit1","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. Chem."},{"key":"ref2\/cit2","doi-asserted-by":"crossref","first-page":"2234","DOI":"10.1021\/jp807701h","volume":"113","author":"Deng Y. Q.","year":"2009","journal-title":"J. Phys. Chem. B"},{"key":"ref3\/cit3","doi-asserted-by":"crossref","first-page":"10570","DOI":"10.1021\/ja034676g","volume":"125","author":"Talhout R.","year":"2003","journal-title":"J. Am. Chem. Soc."},{"key":"ref4\/cit4","doi-asserted-by":"crossref","first-page":"518","DOI":"10.2174\/15734099113096660036","volume":"9","author":"Dubey K. D.","year":"2013","journal-title":"Curr. Comput. Aided Drug Des."},{"key":"ref5\/cit5","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1007\/s10822-011-9484-3","volume":"25","author":"Anisimov V. M.","year":"2011","journal-title":"J. Comput. Aided Mol. Des."},{"key":"ref6\/cit6","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":"ref7\/cit7","doi-asserted-by":"crossref","first-page":"4040","DOI":"10.1021\/jm049081q","volume":"48","author":"Kuhn B.","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref8\/cit8","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1023\/A:1007930623000","volume":"12","author":"Hansson T.","year":"1998","journal-title":"J. Comput. Aided Mol. Des."},{"key":"ref9\/cit9","doi-asserted-by":"crossref","first-page":"12562","DOI":"10.1073\/pnas.202427399","volume":"99","author":"Laio A.","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref10\/cit10","doi-asserted-by":"crossref","first-page":"2810","DOI":"10.1002\/jcc.21860","volume":"32","author":"Kokubo H.","year":"2011","journal-title":"J. Comput. Chem."},{"key":"ref11\/cit11","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/0009-2614(74)80109-0","volume":"28","author":"Torrie G. M.","year":"1974","journal-title":"Chem. Phys. Lett."},{"key":"ref12\/cit12","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/0021-9991(77)90121-8","volume":"23","author":"Torrie G. M.","year":"1977","journal-title":"J. Comput. Phys."},{"key":"ref13\/cit13","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1021\/ct2000638","volume":"7","author":"Buch I.","year":"2011","journal-title":"J. Chem. Theory Comput."},{"key":"ref14\/cit14","doi-asserted-by":"crossref","first-page":"2466","DOI":"10.1016\/j.bpj.2011.03.052","volume":"100","author":"Chen P. C.","year":"2011","journal-title":"Biophys. J."},{"key":"ref15\/cit15","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.ijpharm.2012.03.049","volume":"431","author":"Feenstra P.","year":"2012","journal-title":"Int. J. Pharm."},{"key":"ref16\/cit16","doi-asserted-by":"crossref","first-page":"4816","DOI":"10.1002\/aic.14220","volume":"59","author":"Marzinek J. K.","year":"2013","journal-title":"AIChE J."},{"key":"ref17\/cit17","doi-asserted-by":"crossref","first-page":"6825","DOI":"10.1073\/pnas.0409005102","volume":"102","author":"Woo H. J.","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref18\/cit18","doi-asserted-by":"crossref","first-page":"4824","DOI":"10.1002\/aic.14221","volume":"59","author":"Zhao Y.","year":"2013","journal-title":"AIChE J."},{"key":"ref19\/cit19","doi-asserted-by":"crossref","first-page":"1224","DOI":"10.1002\/jps.23895","volume":"103","author":"Zhao Y.","year":"2014","journal-title":"J. Pharm. Sci."},{"key":"ref20\/cit20","first-page":"A177","volume":"74","author":"Izrailev S.","year":"1998","journal-title":"Biophys. J."},{"key":"ref21\/cit21","doi-asserted-by":"crossref","first-page":"7453","DOI":"10.1021\/jp401508w","volume":"117","author":"Yu T.","year":"2013","journal-title":"J. Phys. Chem. A"},{"key":"ref22\/cit22","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1007\/s00894-012-1609-7","volume":"19","author":"He J.","year":"2013","journal-title":"J. Mol. Model."},{"key":"ref23\/cit23","doi-asserted-by":"crossref","first-page":"e39360","DOI":"10.1371\/journal.pone.0039360","volume":"7","author":"Skovstrup S.","year":"2012","journal-title":"PLoS One"},{"key":"ref24\/cit24","doi-asserted-by":"crossref","first-page":"342","DOI":"10.2174\/157489312803901009","volume":"7","author":"Li M. S.","year":"2012","journal-title":"Curr. Bioinform."},{"key":"ref25\/cit25","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1103\/PhysRevLett.78.2690","volume":"78","author":"Jarzynski C.","year":"1997","journal-title":"Phys. Rev. Lett."},{"key":"ref26\/cit26","doi-asserted-by":"crossref","first-page":"2236","DOI":"10.1021\/ci100346s","volume":"50","author":"Mai B. K.","year":"2010","journal-title":"J. Chem. Inf. Model."},{"key":"ref27\/cit27","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1016\/j.bbrc.2011.06.057","volume":"410","author":"Mai B. K.","year":"2011","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref28\/cit28","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1016\/0022-2836(92)91058-W","volume":"226","author":"Stickle D. F.","year":"1992","journal-title":"J. Mol. Biol."},{"key":"ref29\/cit29","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1016\/S0006-3495(98)77529-0","volume":"75","author":"Pace C. N.","year":"1998","journal-title":"Biophys. J."},{"key":"ref30\/cit30","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1126\/science.347575","volume":"200","author":"Bell G. I.","year":"1978","journal-title":"Science"},{"key":"ref31\/cit31","doi-asserted-by":"crossref","first-page":"1568","DOI":"10.1016\/S0006-3495(97)78804-0","volume":"72","author":"Izrailev S.","year":"1997","journal-title":"Biophys. J."},{"key":"ref32\/cit32","doi-asserted-by":"crossref","first-page":"034701","DOI":"10.1063\/1.4815869","volume":"114","author":"Sekatskii S. K.","year":"2013","journal-title":"J. Appl. Phys."},{"key":"ref33\/cit33","doi-asserted-by":"crossref","first-page":"026108","DOI":"10.1103\/PhysRevE.77.026108","volume":"77","author":"Husson J.","year":"2008","journal-title":"Phys. Rev. E"},{"key":"ref34\/cit34","doi-asserted-by":"crossref","first-page":"108101","DOI":"10.1103\/PhysRevLett.96.108101","volume":"96","author":"Dudko O. K.","year":"2006","journal-title":"Phys. Rev. Lett."},{"key":"ref35\/cit35","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1063\/1.555833","volume":"18","author":"Sangster J.","year":"1989","journal-title":"J. Phys. Chem. Ref. Data"},{"key":"ref36\/cit36","unstructured":"ChemSpider, CSID: 58575.http:\/\/www.chemspider.com\/Chemical-Structure.58575.html(accessed April 18, 2014) ."},{"key":"ref37\/cit37","first-page":"1249","volume":"36","author":"Perrissoud D.","year":"1986","journal-title":"Arzneim.-Forsch."},{"key":"ref38\/cit38","unstructured":"ChemSpider\u2014The free chemical database. Accessible via the Internet athttp:\/\/www.chemspider.com; ID 305, 2013."},{"key":"ref39\/cit39","unstructured":"Data for Biochemical Research. ZirChrom Separations, Inc.; Retrieved Jan. 11, 2012."},{"key":"ref40\/cit40","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"Pettersen E. F.","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref41\/cit41","unstructured":"ParamChem Interface; available via the Internet athttps:\/\/www.paramchem.org."},{"key":"ref42\/cit42","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1002\/jcc.21367","volume":"31","author":"Vanommeslaeghe K.","year":"2010","journal-title":"J. Comput. Chem."},{"key":"ref43\/cit43","doi-asserted-by":"crossref","first-page":"611a","DOI":"10.1016\/j.bpj.2010.12.3519","volume":"100","author":"Vanommeslaeghe K.","year":"2011","journal-title":"Biophys. J."},{"key":"ref44\/cit44","doi-asserted-by":"crossref","first-page":"3155","DOI":"10.1021\/ci3003649","volume":"52","author":"Vanommeslaeghe K.","year":"2012","journal-title":"J. Chem. Inf. Model."},{"key":"ref45\/cit45","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","volume":"4","author":"Hess B.","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"ref46\/cit46","volume-title":"The PyMOL. Molecular Graphics System, Version 1.5.0.4","year":"2012"},{"key":"ref47\/cit47","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1002\/humu.20652","volume":"29","author":"Szeverenyi I.","year":"2008","journal-title":"Hum. Mutat."},{"key":"ref48\/cit48","first-page":"459","volume":"6","author":"Bjelkmar P.","year":"2010","journal-title":"J. Comput. Chem."},{"key":"ref49\/cit49","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":"ref50\/cit50","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","volume":"18","author":"Hess B.","year":"1997","journal-title":"J. Comput. Chem."},{"key":"ref51\/cit51","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":"ref52\/cit52","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","volume":"103","author":"Essmann U.","year":"1995","journal-title":"J. Chem. Phys."},{"key":"ref53\/cit53","doi-asserted-by":"crossref","first-page":"014101","DOI":"10.1063\/1.2408420","volume":"126","author":"Bussi G.","year":"2007","journal-title":"J. Chem. Phys."},{"key":"ref54\/cit54","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1103\/PhysRevLett.45.1196","volume":"45","author":"Parrinello M.","year":"1980","journal-title":"Phys. Rev. Lett."},{"key":"ref55\/cit55","doi-asserted-by":"crossref","first-page":"1881","DOI":"10.1021\/bi00406a013","volume":"27","author":"Cistola D. P.","year":"1988","journal-title":"Biochemistry (Moscow)"},{"key":"ref56\/cit56","doi-asserted-by":"crossref","first-page":"1373","DOI":"10.5012\/bkcs.2009.30.6.1373","volume":"30","author":"Kim H.","year":"2009","journal-title":"Bull. Korean Chem. Soc."},{"key":"ref57\/cit57","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1002\/jcc.540160303","volume":"16","author":"Eisenhaber F.","year":"1995","journal-title":"J. Comput. Chem."},{"key":"ref58\/cit58","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1002\/jcc.540130812","volume":"13","author":"Kumar S.","year":"1992","journal-title":"J. Comput. Chem."},{"key":"ref59\/cit59","doi-asserted-by":"crossref","first-page":"9933","DOI":"10.1039\/c2sm26315g","volume":"8","author":"Donlon L.","year":"2012","journal-title":"Soft Matter."},{"key":"ref60\/cit60","doi-asserted-by":"crossref","first-page":"1924","DOI":"10.1039\/c3sm52257a","volume":"10","author":"Hane F. T.","year":"2014","journal-title":"Soft Matter."},{"key":"ref61\/cit61","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1016\/j.micron.2006.06.014","volume":"38","author":"Lee C. K.","year":"2007","journal-title":"Micron"},{"key":"ref62\/cit62","doi-asserted-by":"crossref","first-page":"9972","DOI":"10.1073\/pnas.97.18.9972","volume":"97","author":"Schwesinger F.","year":"2000","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref63\/cit63","doi-asserted-by":"crossref","first-page":"16638","DOI":"10.1073\/pnas.0505208102","volume":"102","author":"Sulchek T. A.","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref64\/cit64","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.idairyj.2005.01.007","volume":"16","author":"Barbana C.","year":"2006","journal-title":"Int. Dairy J."},{"key":"ref65\/cit65","doi-asserted-by":"crossref","first-page":"27045","DOI":"10.1016\/S0021-9258(19)61478-X","volume":"275","author":"Balendiran G. K.","year":"2000","journal-title":"J. Biol. Chem."},{"key":"ref66\/cit66","doi-asserted-by":"crossref","first-page":"1602","DOI":"10.1016\/j.jpba.2006.02.004","volume":"41","author":"Frazier R. A.","year":"2006","journal-title":"J. Pharm. Biomed. Anal."},{"key":"ref67\/cit67","doi-asserted-by":"crossref","first-page":"23124","DOI":"10.1074\/jbc.M110.110403","volume":"285","author":"Lacal J.","year":"2010","journal-title":"J. Biol. Chem."}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/ci500164q","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,29]],"date-time":"2024-05-29T09:49:36Z","timestamp":1716976176000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/ci500164q"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,7,17]]},"references-count":67,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2014,7,28]]}},"alternative-id":["10.1021\/ci500164q"],"URL":"https:\/\/doi.org\/10.1021\/ci500164q","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,7,17]]}}}