{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T06:44:01Z","timestamp":1782888241148,"version":"3.54.5"},"reference-count":84,"publisher":"American Chemical Society (ACS)","issue":"23","license":[{"start":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T00:00:00Z","timestamp":1764028800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T00:00:00Z","timestamp":1764028800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T00:00:00Z","timestamp":1764028800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100005616","name":"Memorial University of Newfoundland","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005616","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Theory Comput."],"published-print":{"date-parts":[[2025,12,9]]},"DOI":"10.1021\/acs.jctc.5c01402","type":"journal-article","created":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T13:04:48Z","timestamp":1764075888000},"page":"12356-12370","source":"Crossref","is-referenced-by-count":1,"title":["Covalent: Interpretable and Discriminative Collective Variables Reveal Ligand-Dependent Switching in Human Cellular Retinol-Binding Protein 2"],"prefix":"10.1021","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1145-5142","authenticated-orcid":true,"given":"Myongin","family":"Oh","sequence":"first","affiliation":[{"name":"Department of Chemistry, Faculty of Science, Memorial University of Newfoundland, 45 Arctic Ave, St. John\u2019s, Newfoundland A1C 5S7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changin","family":"Oh","sequence":"additional","affiliation":[{"name":"Department of Mathematics, Faculty of Science, Toronto Metropolitan University, 350 Victoria St, Toronto, Ontario M5B 2K3, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eshra","family":"Tabassum","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Faculty of Science, Memorial University of Newfoundland, 45 Arctic Ave, St. John\u2019s, Newfoundland A1C 5S7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2025,11,25]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1038\/nsb0902-646"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1021\/acsbiomaterials.3c00942"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.5b01684"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2013.11.2300"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1042\/BST20200193"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1021\/jp068587c"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.9b00118"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-020-0342-4"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpclett.4c02352"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1038\/s42254-020-0153-0"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2019.00025"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1063\/1.5029972"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1140\/epjb\/s10051-021-00220-w"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1039\/D2RA03660F"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1063\/5.0156343"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.3c05284"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpclett.3c03542"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpclett.0c00535"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2024.06.024"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1080\/00268976.2020.1737742"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1063\/5.0245177"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.4c08824"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-48567-9"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-51970-x"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1038\/nature13241"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03782-y"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.3390\/molecules24112097"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.3390\/nu8110676"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.3390\/nu5093563"},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.3390\/nu14061312"},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.1080\/10409238.2020.1768207"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbalip.2022.159179"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aay8937"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1016\/j.jlr.2021.100054"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-022-03416-7"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1002\/prot.21848"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1063\/1.445869"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1063\/1.466711"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4067"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b00935"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21287"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20945"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1063\/5.0014475"},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(77)90098-5"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1016\/S0969-2126(99)80033-1"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1063\/1.470117"},{"key":"ref48\/cit48","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.9b00358"},{"key":"ref49\/cit49","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.1202.3725"},{"key":"ref50\/cit50","volume-title":"Advances in Neural Information Processing Systems","author":"He X.","year":"2005"},{"key":"ref51\/cit51","doi-asserted-by":"publisher","DOI":"10.1109\/ICSMC.1997.637339"},{"key":"ref52\/cit52","doi-asserted-by":"crossref","first-page":"1942","DOI":"10.1109\/ICNN.1995.488968","volume-title":"Proceedings of ICNN\u201995-international conference on neural networks","volume":"4","author":"Kennedy J.","year":"1995"},{"key":"ref53\/cit53","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1109\/ICDCSW.2011.20","volume-title":"2011 31st international conference on distributed computing systems workshops","author":"Satopaa V.","year":"2011"},{"key":"ref54\/cit54","doi-asserted-by":"publisher","DOI":"10.21105\/joss.00613"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1109\/TKDE.2018.2861858"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.3390\/math13010061"},{"key":"ref57\/cit57","first-page":"2825","volume":"12","author":"Pedregosa F.","year":"2011","journal-title":"J. Mach. Learn. Res."},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.100.020603"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1080\/00268976.2013.813594"},{"key":"ref60\/cit60","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.4c05604"},{"key":"ref61\/cit61","doi-asserted-by":"publisher","DOI":"10.1002\/cphc.202200491"},{"key":"ref62\/cit62","doi-asserted-by":"publisher","DOI":"10.1063\/1.4834695"},{"key":"ref63\/cit63","doi-asserted-by":"publisher","DOI":"10.1063\/1.4811489"},{"key":"ref64\/cit64","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b00743"},{"key":"ref65\/cit65","doi-asserted-by":"publisher","DOI":"10.1007\/s10489-022-03395-6"},{"key":"ref66\/cit66","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00182"},{"key":"ref67\/cit67","doi-asserted-by":"publisher","DOI":"10.1063\/1.4998598"},{"key":"ref68\/cit68","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.3c00526"},{"key":"ref69\/cit69","doi-asserted-by":"publisher","DOI":"10.1063\/1.5025487"},{"key":"ref70\/cit70","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.1c02081"},{"key":"ref71\/cit71","doi-asserted-by":"publisher","DOI":"10.1107\/S1399004714023839"},{"key":"ref72\/cit72","doi-asserted-by":"publisher","DOI":"10.1016\/0079-6107(84)90007-5"},{"key":"ref73\/cit73","doi-asserted-by":"publisher","DOI":"10.1016\/j.abb.2018.03.020"},{"key":"ref74\/cit74","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-015-0531-2"},{"key":"ref75\/cit75","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14561"},{"key":"ref76\/cit76","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.3883"},{"key":"ref77\/cit77","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1993.1239"},{"key":"ref78\/cit78","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0036772"},{"key":"ref79\/cit79","doi-asserted-by":"publisher","DOI":"10.1063\/1.5083040"},{"key":"ref80\/cit80","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.235"},{"key":"ref81\/cit81","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07487-w"},{"key":"ref82\/cit82","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.9b05578"},{"key":"ref83\/cit83","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2313360121"},{"key":"ref84\/cit84","doi-asserted-by":"publisher","DOI":"10.1021\/acs.chemrev.0c01195"}],"container-title":["Journal of Chemical Theory and Computation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jctc.5c01402","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jctc.5c01402","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,9]],"date-time":"2025-12-09T11:10:44Z","timestamp":1765278644000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jctc.5c01402"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,25]]},"references-count":84,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2025,12,9]]}},"alternative-id":["10.1021\/acs.jctc.5c01402"],"URL":"https:\/\/doi.org\/10.1021\/acs.jctc.5c01402","relation":{},"ISSN":["1549-9618","1549-9626"],"issn-type":[{"value":"1549-9618","type":"print"},{"value":"1549-9626","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,25]]}}}