{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T11:44:55Z","timestamp":1763466295980,"version":"3.45.0"},"reference-count":98,"publisher":"American Chemical Society (ACS)","issue":"23","license":[{"start":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T00:00:00Z","timestamp":1763424000000},"content-version":"vor","delay-in-days":365,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["1U01CA258512-01"],"award-info":[{"award-number":["1U01CA258512-01"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007863","name":"Rice University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007863","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2024,12,9]]},"DOI":"10.1021\/acs.jcim.4c01278","type":"journal-article","created":{"date-parts":[[2024,11,18]],"date-time":"2024-11-18T08:36:42Z","timestamp":1731919002000},"page":"8729-8742","source":"Crossref","is-referenced-by-count":0,"title":["RankMHC: Learning to Rank Class-I Peptide-MHC Structural Models"],"prefix":"10.1021","volume":"64","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7106-6689","authenticated-orcid":true,"given":"Romanos","family":"Fasoulis","sequence":"first","affiliation":[{"name":"Department of Computer Science","place":["Houston, United States"]},{"name":"Rice University","place":["Houston, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Georgios","family":"Paliouras","sequence":"additional","affiliation":[{"name":"Institute of Informatics and Telecommunications","place":["Athens, Greece"]},{"name":"NCSR Demokritos","place":["Athens, Greece"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0699-8038","authenticated-orcid":true,"given":"Lydia E.","family":"Kavraki","sequence":"additional","affiliation":[{"name":"Department of Computer Science","place":["Houston, United States"]},{"name":"Rice University","place":["Houston, United States"]},{"name":"Ken Kennedy Institute","place":["Houston, United States"]},{"name":"Rice University","place":["Houston, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"316","published-online":{"date-parts":[[2024,11,18]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-immunol-082119-124838"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.712488"},{"key":"ref3\/cit3","doi-asserted-by":"crossref","unstructured":"Bassani-Sternberg, M.\n                      Peptidomics\n                      ; Springer: New York, 2018; pp 209\u2013221.","DOI":"10.1007\/978-1-4939-7537-2_14"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2111815118"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa379"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2020.06.010"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(93)90490-H"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1016\/0952-7915(94)90028-0"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.iy.13.040195.003103"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymthe.2018.12.010"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1038\/s41589-020-0610-1"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-32811-1"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1093\/discim\/kyac001"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34896-0"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2312057120"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.235"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh042"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp946"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1038\/sdata.2018.212"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3730"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1016\/j.drudis.2018.05.006"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-018-2449-y"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03819-2"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.1c01114"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad1011"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07487-w"},{"key":"ref27\/cit27","doi-asserted-by":"crossref","unstructured":"Perez, M. A. S.; Cuendet, M. A.; R\u00f6hrig, U. F.; Michielin, O.; Zoete, V.\n                      Computational Peptide Science\n                      ; Springer: US, 2022; pp 245\u2013282.","DOI":"10.1007\/978-1-0716-1855-4_13"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.2174\/1568026619666181224101744"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1007\/s12551-013-0130-2"},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.1007\/s12539-019-00327-w"},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540130412"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1063\/1.445869"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1016\/j.drudis.2007.07.006"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1023\/A:1008040323669"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1999.3371"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1038\/srep18413"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21334"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.3390\/molecules24050881"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.3c01667"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0155183"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.878762"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi0506s15"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00125"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1021\/ci500393h"},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.02047"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbagen.2020.129535"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1225"},{"key":"ref48\/cit48","unstructured":"St\u00e4rk, H.; Ganea, O.; Pattanaik, L.; Barzilay, R.; Jaakkola, T. Equibind: Geometric deep learning for drug binding structure prediction. In\n                      International Conference on Machine Learning\n                      ; 2022; pp 20503\u201320521."},{"key":"ref49\/cit49","unstructured":"Corso, G.; St\u00e4rk, H.; Jing, B.; Barzilay, R.; Jaakkola, T. DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking. In\n                      International Conference on Learning Representations (ICLR)\n                      ; 2023."},{"key":"ref50\/cit50","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-021-00522-2"},{"key":"ref51\/cit51","doi-asserted-by":"crossref","unstructured":"Ashtawy, H. M.; Mahapatra, N. R.\n                      Lecture Notes in Computer Science\n                      ; Springer International Publishing: 2014; pp 15\u201332.","DOI":"10.1007\/978-3-319-09042-9_2"},{"key":"ref52\/cit52","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-16-S6-S3"},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.1c01510"},{"key":"ref54\/cit54","doi-asserted-by":"publisher","DOI":"10.3389\/fchem.2021.753002"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab474"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.3389\/fbinf.2022.885983"},{"key":"ref57\/cit57","doi-asserted-by":"publisher","DOI":"10.1038\/srep46710"},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-023-00731-x"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1016\/j.jare.2022.07.001"},{"key":"ref60\/cit60","doi-asserted-by":"publisher","DOI":"10.1016\/S0960-894X(01)00021-X"},{"key":"ref61\/cit61","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-14526-x"},{"key":"ref62\/cit62","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.01583"},{"key":"ref63\/cit63","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.1c00056"},{"key":"ref64\/cit64","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx589"},{"key":"ref65\/cit65","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.887759"},{"key":"ref66\/cit66","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-42163-z"},{"key":"ref67\/cit67","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2010.10.030"},{"key":"ref68\/cit68","unstructured":"Burges, C. From RankNet to LambdaRank to LambdaMART: An Overview, 2010."},{"key":"ref69\/cit69","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-015-0052-z"},{"key":"ref70\/cit70","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw244"},{"key":"ref71\/cit71","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.27193"},{"key":"ref72\/cit72","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005659"},{"volume-title":"NACCESS. Computer Program","year":"1993","author":"Hubbard S.","key":"ref73\/cit73"},{"volume-title":"Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining","year":"2016","author":"Chen T.","key":"ref74\/cit74"},{"key":"ref75\/cit75","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1800914"},{"key":"ref76\/cit76","unstructured":"Bolusani, S.\n                      The SCIP Optimization Suite 9.0\n                      ; Technical Report, 2024."},{"key":"ref77\/cit77","unstructured":"Perron, L.; Didier, F.\n                      CP-SAT\n                      . https:\/\/developers.google.com\/optimization\/cp\/cp_solver\/."},{"key":"ref78\/cit78","doi-asserted-by":"publisher","DOI":"10.1007\/s10791-009-9112-1"},{"volume-title":"Advances in Neural Information Processing Systems","year":"2006","author":"Burges C.","key":"ref79\/cit79"},{"key":"ref80\/cit80","doi-asserted-by":"publisher","DOI":"10.1214\/aos\/1013203451"},{"key":"ref81\/cit81","doi-asserted-by":"publisher","DOI":"10.1107\/S0567739482001806"},{"key":"ref82\/cit82","doi-asserted-by":"crossref","DOI":"10.4324\/9780203726631","volume-title":"Research Design and Statistical Analysis","author":"Myers J. L.","year":"2013"},{"key":"ref83\/cit83","doi-asserted-by":"publisher","DOI":"10.1037\/0021-9010.72.1.146"},{"key":"ref84\/cit84","doi-asserted-by":"publisher","DOI":"10.1214\/aoms\/1177706717"},{"volume-title":"Encyclopedia of Statistical Sciences","year":"2005","author":"Myers L.","key":"ref85\/cit85"},{"key":"ref86\/cit86","doi-asserted-by":"publisher","DOI":"10.1039\/D3DD00227F"},{"key":"ref87\/cit87","doi-asserted-by":"publisher","DOI":"10.1145\/582415.582418"},{"volume-title":"Proceedings of the 29th ACM International Conference on Information and Knowledge Management","year":"2020","author":"Gienapp L.","key":"ref88\/cit88"},{"key":"ref89\/cit89","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa1050"},{"key":"ref90\/cit90","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2018.05.014"},{"volume-title":"2020 3rd International Seminar on Research of Information Technology and Intelligent Systems (ISRITI)","year":"2020","author":"Qomariyah N. N.","key":"ref91\/cit91"},{"key":"ref92\/cit92","first-page":"4768","volume-title":"Proceedings of the 31st International Conference on Neural Information Processing Systems","author":"Lundberg S. M.","year":"2017"},{"key":"ref93\/cit93","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm216"},{"volume-title":"Proceedings of the 22nd international conference on Machine learning - ICML\u201905","year":"2005","author":"Burges C.","key":"ref94\/cit94"},{"key":"ref95\/cit95","unstructured":"Lee, J.; Lee, I.; Kang, J. Self-Attention Graph Pooling. In\n                      Proceedings of the 36th International Conference on Machine Learning\n                      ; 2019."},{"key":"ref96\/cit96","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2023.11.011"},{"key":"ref97\/cit97","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.7b00309"},{"key":"ref98\/cit98","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00411"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.4c01278","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.4c01278","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T11:43:07Z","timestamp":1763466187000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.4c01278"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,18]]},"references-count":98,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2024,12,9]]}},"alternative-id":["10.1021\/acs.jcim.4c01278"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.4c01278","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"type":"print","value":"1549-9596"},{"type":"electronic","value":"1549-960X"}],"subject":[],"published":{"date-parts":[[2024,11,18]]}}}