{"id":"https://openalex.org/W4404473800","doi":"https://doi.org/10.1021/acs.jcim.4c01278","title":"RankMHC: Learning to Rank Class-I Peptide-MHC Structural Models","display_name":"RankMHC: Learning to Rank Class-I Peptide-MHC Structural Models","publication_year":2024,"publication_date":"2024-11-18","ids":{"openalex":"https://openalex.org/W4404473800","doi":"https://doi.org/10.1021/acs.jcim.4c01278","pmid":"https://pubmed.ncbi.nlm.nih.gov/39555889"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01278","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01278","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01278","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01278","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056840325","display_name":"Romanos Fasoulis","orcid":"https://orcid.org/0000-0001-7106-6689"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Romanos Fasoulis","raw_affiliation_strings":["Department of Computer Science","Rice University","Department of Computer Science, Rice University, Houston, Texas 77005, United States"],"raw_orcid":"https://orcid.org/0000-0001-7106-6689","affiliations":[{"raw_affiliation_string":"Department of Computer Science","institution_ids":[]},{"raw_affiliation_string":"Rice University","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, Texas 77005, United States","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010395244","display_name":"\u0393\u03b5\u03ce\u03c1\u03b3\u03b9\u03bf\u03c2 \u03a0\u03b1\u03bb\u03b9\u03bf\u03cd\u03c1\u03b1\u03c2","orcid":"https://orcid.org/0000-0001-9629-2367"},"institutions":[{"id":"https://openalex.org/I203474044","display_name":"National Centre of Scientific Research \"Demokritos\"","ror":"https://ror.org/038jp4m40","country_code":"GR","type":"facility","lineage":["https://openalex.org/I203474044"]},{"id":"https://openalex.org/I4210152232","display_name":"Institute of Informatics of the Slovak Academy of Sciences","ror":"https://ror.org/04jgqpc26","country_code":"SK","type":"facility","lineage":["https://openalex.org/I207624831","https://openalex.org/I4210152232"]},{"id":"https://openalex.org/I4387152169","display_name":"Institute of Informatics & Telecommunications","ror":"https://ror.org/0396t6k89","country_code":null,"type":"facility","lineage":["https://openalex.org/I203474044","https://openalex.org/I4387152169"]}],"countries":["GR","SK"],"is_corresponding":false,"raw_author_name":"Georgios Paliouras","raw_affiliation_strings":["Institute of Informatics and Telecommunications","NCSR Demokritos","Institute of Informatics and Telecommunications, NCSR Demokritos, Athens 15341, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Informatics and Telecommunications","institution_ids":["https://openalex.org/I4210152232","https://openalex.org/I4387152169"]},{"raw_affiliation_string":"NCSR Demokritos","institution_ids":["https://openalex.org/I203474044"]},{"raw_affiliation_string":"Institute of Informatics and Telecommunications, NCSR Demokritos, Athens 15341, Greece","institution_ids":["https://openalex.org/I203474044","https://openalex.org/I4387152169"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067205988","display_name":"Lydia E. Kavraki","orcid":"https://orcid.org/0000-0003-0699-8038"},"institutions":[{"id":"https://openalex.org/I4210094934","display_name":"Kennedy Center","ror":"https://ror.org/00kzzgw26","country_code":"DK","type":"healthcare","lineage":["https://openalex.org/I2802567020","https://openalex.org/I4210094934"]},{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["DK","US"],"is_corresponding":true,"raw_author_name":"Lydia E. Kavraki","raw_affiliation_strings":["Department of Computer Science","Ken Kennedy Institute","Rice University","Department of Computer Science, Rice University, Houston, Texas 77005, United States","Ken Kennedy Institute, Rice University, Houston, Texas 77005, United States"],"raw_orcid":"https://orcid.org/0000-0003-0699-8038","affiliations":[{"raw_affiliation_string":"Department of Computer Science","institution_ids":[]},{"raw_affiliation_string":"Ken Kennedy Institute","institution_ids":["https://openalex.org/I4210094934"]},{"raw_affiliation_string":"Rice University","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, Texas 77005, United States","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Ken Kennedy Institute, Rice University, Houston, Texas 77005, United States","institution_ids":["https://openalex.org/I74775410"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5067205988"],"corresponding_institution_ids":["https://openalex.org/I4210094934","https://openalex.org/I74775410"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.11634181,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"64","issue":"23","first_page":"8729","last_page":"8742"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.7179857492446899},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.570099949836731},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.5505382418632507},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5420731902122498},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5149336457252502},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.4966490864753723},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4917636215686798},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.42288070917129517},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"Ensemble learning","score":0.4195924401283264},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3489644527435303},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30102384090423584},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.18148469924926758},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.15644291043281555},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12219107151031494},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08842575550079346},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08594062924385071}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7179857492446899},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.570099949836731},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.5505382418632507},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5420731902122498},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5149336457252502},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.4966490864753723},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4917636215686798},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42288070917129517},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.4195924401283264},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3489644527435303},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30102384090423584},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.18148469924926758},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.15644291043281555},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12219107151031494},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08842575550079346},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08594062924385071},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.4c01278","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01278","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01278","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:39555889","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39555889","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11633655","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11633655/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11633655/pdf/ci4c01278.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},{"id":"pmh:oai:europepmc.org:11428161","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11633655","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.4c01278","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01278","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01278","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.5199999809265137,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G1960506700","display_name":"PROTEAN-CR: Proteomics Toolkit for Ensemble Analysis in Cancer Research","funder_award_id":"5u01ca258512-03","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8946597769","display_name":null,"funder_award_id":"U01 CA258512","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G940880656","display_name":null,"funder_award_id":"1U01CA258512-01","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320310133","display_name":"Rice University","ror":"https://ror.org/008zs3103"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4404473800.pdf","grobid_xml":"https://content.openalex.org/works/W4404473800.grobid-xml"},"referenced_works_count":93,"referenced_works":["https://openalex.org/W156083275","https://openalex.org/W175958581","https://openalex.org/W569478347","https://openalex.org/W1497260480","https://openalex.org/W1539550814","https://openalex.org/W1539947917","https://openalex.org/W1583837637","https://openalex.org/W1602136775","https://openalex.org/W1607931568","https://openalex.org/W1678356000","https://openalex.org/W1950993160","https://openalex.org/W1976499671","https://openalex.org/W1978499958","https://openalex.org/W1980054394","https://openalex.org/W1981987799","https://openalex.org/W1991731171","https://openalex.org/W2000861313","https://openalex.org/W2003356525","https://openalex.org/W2022231632","https://openalex.org/W2049380243","https://openalex.org/W2053174787","https://openalex.org/W2069870183","https://openalex.org/W2105321472","https://openalex.org/W2116494521","https://openalex.org/W2116528443","https://openalex.org/W2122339645","https://openalex.org/W2130479394","https://openalex.org/W2131363383","https://openalex.org/W2134967712","https://openalex.org/W2159404298","https://openalex.org/W2162059449","https://openalex.org/W2171234651","https://openalex.org/W2388080941","https://openalex.org/W2399366904","https://openalex.org/W2419892062","https://openalex.org/W2606439133","https://openalex.org/W2608559058","https://openalex.org/W2743893844","https://openalex.org/W2754641896","https://openalex.org/W2774371249","https://openalex.org/W2792688048","https://openalex.org/W2800677598","https://openalex.org/W2891197287","https://openalex.org/W2897326603","https://openalex.org/W2904572271","https://openalex.org/W2909834406","https://openalex.org/W2911741628","https://openalex.org/W2912083425","https://openalex.org/W2914874661","https://openalex.org/W2919975879","https://openalex.org/W2921473648","https://openalex.org/W2949223833","https://openalex.org/W2952607757","https://openalex.org/W2968781851","https://openalex.org/W2973523639","https://openalex.org/W2990138404","https://openalex.org/W2999170959","https://openalex.org/W3005844923","https://openalex.org/W3024570138","https://openalex.org/W3042910002","https://openalex.org/W3044163929","https://openalex.org/W3049184299","https://openalex.org/W3082411326","https://openalex.org/W3114418016","https://openalex.org/W3159821165","https://openalex.org/W3168430821","https://openalex.org/W3177828909","https://openalex.org/W3201078782","https://openalex.org/W3201869122","https://openalex.org/W3209909976","https://openalex.org/W3210807621","https://openalex.org/W3217568487","https://openalex.org/W4220798728","https://openalex.org/W4224291667","https://openalex.org/W4224866864","https://openalex.org/W4229026733","https://openalex.org/W4229451133","https://openalex.org/W4232437429","https://openalex.org/W4247950230","https://openalex.org/W4283013935","https://openalex.org/W4283390471","https://openalex.org/W4287448187","https://openalex.org/W4295514007","https://openalex.org/W4309900050","https://openalex.org/W4320341731","https://openalex.org/W4383067148","https://openalex.org/W4387491415","https://openalex.org/W4388464011","https://openalex.org/W4389611046","https://openalex.org/W4389920712","https://openalex.org/W4390886467","https://openalex.org/W4392240303","https://openalex.org/W4396721167"],"related_works":["https://openalex.org/W3129816939","https://openalex.org/W2912862995","https://openalex.org/W2985427592","https://openalex.org/W2101501829","https://openalex.org/W2400569965","https://openalex.org/W2060263731","https://openalex.org/W2003194288","https://openalex.org/W391093122","https://openalex.org/W1521239975","https://openalex.org/W4361305867"],"abstract_inverted_index":{"The":[0],"binding":[1,130,183,198,231],"of":[2,36,46,66,86,95,124,172,212,215],"peptides":[3],"to":[4,26,29,119,143,206],"class-I":[5],"Major":[6],"Histocompability":[7],"Complex":[8],"(MHC)":[9],"receptors":[10,18],"and":[11,55],"their":[12],"subsequent":[13],"recognition":[14],"downstream":[15],"by":[16,158],"T-cell":[17],"are":[19,163,168],"crucial":[20],"processes":[21],"for":[22,49,53],"most":[23,122,170,209],"multicellular":[24],"organisms":[25],"be":[27,120,240],"able":[28],"fight":[30],"various":[31],"diseases.":[32],"Thus,":[33],"the":[34,64,87,100,114,121,125,129,134,138,152,165,169,173,181,208],"identification":[35,83,185,200],"peptide":[37,81,97,135,153,182],"antigens":[38],"that":[39,132,140,167,237,248],"can":[40,239],"elicit":[41],"an":[42,93,144,195,213],"immune":[43],"response":[44],"is":[45,141,148,203],"immense":[47],"importance":[48,65],"developing":[50],"successful":[51],"therapies":[52],"bacterial":[54],"viral":[56],"infections,":[57],"even":[58],"cancer.":[59],"Recently,":[60],"studies":[61],"have":[62],"demonstrated":[63],"peptide-MHC":[67],"(pMHC)":[68],"structural":[69,73,89,245,251],"analysis,":[70],"with":[71,105,113,242],"pMHC":[72,88,197,216,244],"modeling":[74,90,246,252],"methods":[75],"gradually":[76],"becoming":[77],"more":[78],"popular":[79],"in":[80,99],"antigen":[82],"workflows.":[84],"Most":[85],"tools":[91,247],"provide":[92],"ensemble":[94,139,214],"candidate":[96],"poses":[98,154],"MHC-I":[101],"cleft,":[102],"each":[103],"associated":[104],"a":[106,110,159,188],"score":[107],"stemming":[108],"from":[109,137],"scoring":[111,116,161,222],"function,":[112],"top":[115],"pose":[117,136,184,232],"assumed":[118],"representative":[123,171],"ensemble.":[126],"However,":[127],"identifying":[128],"mode,":[131],"is,":[133],"closer":[142],"unavailable":[145],"native":[146],"structure,":[147],"not":[149,164],"trivial.":[150],"Oftentimes,":[151],"characterized":[155],"as":[156,187,224,226],"best":[157],"protein-ligand":[160],"function":[162],"ones":[166],"actual":[174],"structure.":[175],"In":[176],"this":[177],"work,":[178],"we":[179],"frame":[180],"problem":[186],"Learning-to-Rank":[189],"(LTR)":[190],"problem.":[191],"We":[192,234],"present":[193],"RankMHC,":[194],"LTR-based":[196],"mode":[199],"predictor,":[201],"which":[202],"specifically":[204],"trained":[205],"predict":[207],"accurate":[210],"ranking":[211],"conformations.":[217],"RankMHC":[218,238],"outperforms":[219],"classical":[220],"peptide-ligand":[221],"functions,":[223],"well":[225],"previous":[227],"Machine":[228],"Learning":[229],"(ML)-based":[230],"predictors.":[233],"further":[235],"demonstrate":[236],"used":[241],"many":[243],"use":[249],"different":[250],"protocols.":[253]},"counts_by_year":[],"updated_date":"2026-08-24T07:32:12.397491","created_date":"2025-10-10T00:00:00"}