{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T16:18:54Z","timestamp":1787761134280,"version":"build-2784847793"},"reference-count":42,"publisher":"Royal Society of Chemistry (RSC)","issue":"33","license":[{"start":{"date-parts":[[2027,7,27]],"date-time":"2027-07-27T00:00:00Z","timestamp":1816646400000},"content-version":"am","delay-in-days":572,"URL":"http:\/\/rsc.li\/journals-terms-of-use"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22203089"],"award-info":[{"award-number":["22203089"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22573043"],"award-info":[{"award-number":["22573043"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100018617","name":"Liaoning Revitalization Talents Program","doi-asserted-by":"publisher","award":["XLYC2402023"],"award-info":[{"award-number":["XLYC2402023"]}],"id":[{"id":"10.13039\/501100018617","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["rsc.org"],"crossmark-restriction":true},"short-container-title":["Phys. Chem. Chem. Phys."],"abstract":"<jats:p>MD simulations reveal that PTM-induced energetic, correlated-motion, and structural changes act cooperatively to regulate pMHC binding.<\/jats:p>","DOI":"10.1039\/d6cp02308h","type":"journal-article","created":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T11:42:53Z","timestamp":1785152573000},"page":"20276-20288","update-policy":"https:\/\/doi.org\/10.1039\/rsc_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A predictive multiscale framework for post-translational modification-dependent peptide\u2013MHC class I binding"],"prefix":"10.1039","volume":"28","author":[{"given":"Xiaoning","family":"Yao","sequence":"first","affiliation":[{"name":"School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, China"},{"name":"Interdisciplinary Research Center for Biology and Chemistry, Liaoning Normal University, Dalian, 116029, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Gang","sequence":"additional","affiliation":[{"name":"School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, China"},{"name":"Interdisciplinary Research Center for Biology and Chemistry, Liaoning Normal University, Dalian, 116029, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaoyue","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, China"},{"name":"Interdisciplinary Research Center for Biology and Chemistry, Liaoning Normal University, Dalian, 116029, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhihui","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, China"},{"name":"Interdisciplinary Research Center for Biology and Chemistry, Liaoning Normal University, Dalian, 116029, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujie","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, China"},{"name":"Interdisciplinary Research Center for Biology and Chemistry, Liaoning Normal University, Dalian, 116029, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuo","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, China"},{"name":"Interdisciplinary Research Center for Biology and Chemistry, Liaoning Normal University, Dalian, 116029, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiying","family":"Chu","sequence":"additional","affiliation":[{"name":"Interdisciplinary Research Center for Biology and Chemistry, Liaoning Normal University, Dalian, 116029, China"},{"name":"Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8223-705X","authenticated-orcid":false,"given":"Guohui","family":"Li","sequence":"additional","affiliation":[{"name":"Interdisciplinary Research Center for Biology and Chemistry, Liaoning Normal University, Dalian, 116029, China"},{"name":"Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4041-9095","authenticated-orcid":false,"given":"Anhui","family":"Wang","sequence":"additional","affiliation":[{"name":"Interdisciplinary Research Center for Biology and Chemistry, Liaoning Normal University, Dalian, 116029, China"},{"name":"Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"292","published-online":{"date-parts":[[2026]]},"reference":[{"key":"D6CP02308H\/cit1\/1","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1146\/annurev-immunol-032712-095910","volume":"31","author":"Blum","year":"2013","journal-title":"Annu. Rev. Immunol."},{"key":"D6CP02308H\/cit2\/1","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1038\/s41577-022-00707-2","volume":"22","author":"Pishesha","year":"2022","journal-title":"Nat. Rev. Immunol."},{"key":"D6CP02308H\/cit3\/1","doi-asserted-by":"crossref","first-page":"335","DOI":"10.3389\/fimmu.2015.00335","volume":"6","author":"Adiko","year":"2015","journal-title":"Front. Immunol."},{"key":"D6CP02308H\/cit4\/1","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1016\/j.immuni.2023.03.009","volume":"56","author":"Racle","year":"2023","journal-title":"Immunity"},{"key":"D6CP02308H\/cit5\/1","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.molimm.2012.10.020","volume":"55","author":"Eisenlohr","year":"2013","journal-title":"Mol. Immunol."},{"key":"D6CP02308H\/cit6\/1","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.semcancer.2019.03.005","volume":"66","author":"M\u00fcnz","year":"2020","journal-title":"Semin. Cancer Biol."},{"key":"D6CP02308H\/cit7\/1","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1038\/ni1516","volume":"8","author":"Jensen","year":"2007","journal-title":"Nat. Immunol."},{"key":"D6CP02308H\/cit8\/1","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/S0065-2776(01)78006-6","volume":"78","author":"Kastrup","year":"2001","journal-title":"Adv. Immunol."},{"key":"D6CP02308H\/cit9\/1","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/S1471-4906(01)01976-7","volume":"22","author":"Doyle","year":"2001","journal-title":"Trends Immunol."},{"key":"D6CP02308H\/cit10\/1","doi-asserted-by":"crossref","first-page":"2569","DOI":"10.1084\/jem.20131241","volume":"210","author":"Scally","year":"2013","journal-title":"J. Exp. Med."},{"key":"D6CP02308H\/cit11\/1","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1038\/s41587-022-01464-2","volume":"41","author":"Kacen","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"D6CP02308H\/cit12\/1","doi-asserted-by":"crossref","first-page":"1800041","DOI":"10.1002\/pmic.201800041","volume":"18","author":"Marino","year":"2018","journal-title":"Proteomics"},{"key":"D6CP02308H\/cit13\/1","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1073\/pnas.92.3.753","volume":"92","author":"Rognan","year":"1995","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"D6CP02308H\/cit14\/1","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.coi.2020.04.004","volume":"64","author":"Margulies","year":"2020","journal-title":"Curr. Opin. Immunol."},{"key":"D6CP02308H\/cit15\/1","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1016\/j.molcel.2018.12.018","volume":"73","author":"Wu","year":"2019","journal-title":"Mol. Cell"},{"key":"D6CP02308H\/cit16\/1","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1002\/bip.21078","volume":"91","author":"Yaneva","year":"2009","journal-title":"Biopolymers"},{"key":"D6CP02308H\/cit17\/1","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1080\/08927020802256298","volume":"34","author":"Omasits","year":"2008","journal-title":"Mol. Simul."},{"key":"D6CP02308H\/cit18\/1","doi-asserted-by":"crossref","first-page":"1991","DOI":"10.1021\/acschembio.4c00312","volume":"19","author":"Kelly","year":"2024","journal-title":"ACS Chem. Biol."},{"key":"D6CP02308H\/cit19\/1","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1038\/nchembio.495","volume":"7","author":"Zhang","year":"2011","journal-title":"Nat. Chem. Biol."},{"key":"D6CP02308H\/cit20\/1","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nrg3173","volume":"13","author":"Greer","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"D6CP02308H\/cit21\/1","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1038\/nrm3841","volume":"15","author":"Choudhary","year":"2014","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"D6CP02308H\/cit22\/1","doi-asserted-by":"crossref","first-page":"7538","DOI":"10.1074\/jbc.RA117.000313","volume":"293","author":"Papakyriakou","year":"2018","journal-title":"J. Biol. Chem."},{"key":"D6CP02308H\/cit23\/1","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1007\/s12539-025-00719-1","volume":"17","author":"Xu","year":"2025","journal-title":"Interdiscip. Sci.: Comput. Life Sci."},{"key":"D6CP02308H\/cit24\/1","doi-asserted-by":"crossref","first-page":"2479","DOI":"10.1073\/pnas.92.7.2479","volume":"92","author":"Fremont","year":"1995","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"D6CP02308H\/cit25\/1","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"D6CP02308H\/cit26\/1","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1007\/s12539-024-00643-w","volume":"16","author":"Chiarelli","year":"2024","journal-title":"Interdiscip. Sci.: Comput. Life Sci."},{"key":"D6CP02308H\/cit28\/1","doi-asserted-by":"crossref","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","volume":"11","author":"Maier","year":"2015","journal-title":"J. Chem. Theory Comput."},{"key":"D6CP02308H\/cit29\/1","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1002\/jcc.20035","volume":"25","author":"Wang","year":"2004","journal-title":"J. Comput. Chem."},{"key":"D6CP02308H\/cit30\/1","volume-title":"Gaussian 16","author":"Frisch","year":"2016","unstructured":"M. J.Frisch ,  G. W.Trucks ,  H. B.Schlegel et al. ,  Gaussian 16 ,  Gaussian Inc. ,  Wallingford CT ,  2016"},{"key":"D6CP02308H\/cit31\/1","doi-asserted-by":"crossref","first-page":"1409","DOI":"10.1080\/00268978800101881","volume":"65","author":"Pastor","year":"1988","journal-title":"Mol. Phys."},{"key":"D6CP02308H\/cit32\/1","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1063\/1.448118","volume":"81","author":"Berendsen","year":"1984","journal-title":"J. Chem. Phys."},{"key":"D6CP02308H\/cit33\/1","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","volume":"23","author":"Ryckaert","year":"1977","journal-title":"J. Comput. Phys."},{"key":"D6CP02308H\/cit34\/1","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem. Phys."},{"key":"D6CP02308H\/cit35\/1","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.1021\/ct400341p","volume":"9","author":"Roe","year":"2013","journal-title":"J. Chem. Theory Comput."},{"key":"D6CP02308H\/cit36\/1","author":"Schr\u00f6dinger","year":"2015","unstructured":"L. L. C.Schr\u00f6dinger , The PyMOL Molecular Graphics System, Version 1.8, Schr\u00f6dinger LLC, New York,  2015"},{"key":"D6CP02308H\/cit37\/1","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"D6CP02308H\/cit38\/1","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1002\/prot.340110305","volume":"11","author":"Ichiye","year":"1991","journal-title":"Proteins"},{"key":"D6CP02308H\/cit39\/1","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1002\/prot.340170408","volume":"17","author":"Amadei","year":"1993","journal-title":"Proteins"},{"key":"D6CP02308H\/cit40\/1","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1517\/17460441.2015.1032936","volume":"10","author":"Genheden","year":"2015","journal-title":"Expert Opin. Drug Discov."},{"key":"D6CP02308H\/cit41\/1","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1021\/ci100275a","volume":"51","author":"Hou","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"D6CP02308H\/cit42\/1","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1002\/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A","volume":"20","author":"Weiser","year":"1999","journal-title":"J. Comput. Chem."},{"key":"D6CP02308H\/cit43\/1","doi-asserted-by":"crossref","first-page":"14450","DOI":"10.1039\/C7CP07623A","volume":"20","author":"Sun","year":"2018","journal-title":"Phys. Chem. Chem. Phys."}],"container-title":["Physical Chemistry Chemical Physics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/pubs.rsc.org\/CP\/article-pdf\/doi\/10.1039\/D6CP02308H\/0\/D6CP02308H.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T15:24:20Z","timestamp":1787757860000},"score":1,"resource":{"primary":{"URL":"http:\/\/pubs.rsc.org\/CP\/article-lookup\/doi\/10.1039\/D6CP02308H"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":42,"journal-issue":{"issue":"33","published-print":{"date-parts":[[2026,8,26]]}},"URL":"https:\/\/doi.org\/10.1039\/d6cp02308h","relation":{},"ISSN":["1463-9076","1463-9084"],"issn-type":[{"value":"1463-9076","type":"print"},{"value":"1463-9084","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026]]}}}