{"id":"https://openalex.org/W4366085055","doi":"https://doi.org/10.1093/bib/bbad150","title":"A comprehensive assessment and comparison of tools for HLA class I peptide-binding prediction","display_name":"A comprehensive assessment and comparison of tools for HLA class I peptide-binding prediction","publication_year":2023,"publication_date":"2023-04-17","ids":{"openalex":"https://openalex.org/W4366085055","doi":"https://doi.org/10.1093/bib/bbad150","pmid":"https://pubmed.ncbi.nlm.nih.gov/37068304"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad150","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad150","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad150/50410803/bbad150.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad150/50410803/bbad150.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100377181","display_name":"Meng Wang","orcid":"https://orcid.org/0000-0002-6626-8857"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Meng Wang","raw_affiliation_strings":["School of Computer Science and engineering, Central South University , Changsha 410083 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and engineering, Central South University , Changsha 410083 , China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088423732","display_name":"Lukasz Kurgan","orcid":"https://orcid.org/0000-0002-7749-0314"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lukasz Kurgan","raw_affiliation_strings":["Department of Computer Science, Virginia Commonwealth University , Richmond, VA 23284 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Commonwealth University , Richmond, VA 23284 , USA","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100719013","display_name":"Min Li","orcid":"https://orcid.org/0000-0002-0188-1394"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Min Li","raw_affiliation_strings":["School of Computer Science and engineering, Central South University , Changsha 410083 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and engineering, Central South University , Changsha 410083 , China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5088423732","https://openalex.org/A5100719013"],"corresponding_institution_ids":["https://openalex.org/I139660479","https://openalex.org/I184840846"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.1527,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.8737291,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"24","issue":"3","first_page":null,"last_page":null},"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":0.9965000152587891,"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":0.9943000078201294,"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/benchmark","display_name":"Benchmark (surveying)","score":0.6994751691818237},{"id":"https://openalex.org/keywords/human-leukocyte-antigen","display_name":"Human leukocyte antigen","score":0.6860517263412476},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6668320894241333},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.553374707698822},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48076602816581726},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.46458959579467773},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.4212490916252136},{"id":"https://openalex.org/keywords/predictive-modelling","display_name":"Predictive modelling","score":0.41767364740371704},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41649600863456726},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3549835979938507},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2065584361553192},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.15866512060165405},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.10535001754760742}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6994751691818237},{"id":"https://openalex.org/C188280979","wikidata":"https://www.wikidata.org/wiki/Q911125","display_name":"Human leukocyte antigen","level":3,"score":0.6860517263412476},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6668320894241333},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.553374707698822},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48076602816581726},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.46458959579467773},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.4212490916252136},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.41767364740371704},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41649600863456726},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3549835979938507},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2065584361553192},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.15866512060165405},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.10535001754760742},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"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":"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":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad150","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad150","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad150/50410803/bbad150.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37068304","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37068304","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbad150","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad150","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad150/50410803/bbad150.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4043378463","display_name":null,"funder_award_id":"61832019","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4366085055.pdf"},"referenced_works_count":72,"referenced_works":["https://openalex.org/W1558421445","https://openalex.org/W1972571116","https://openalex.org/W1994048581","https://openalex.org/W2000305183","https://openalex.org/W2027267610","https://openalex.org/W2053707749","https://openalex.org/W2053931156","https://openalex.org/W2073621589","https://openalex.org/W2084492053","https://openalex.org/W2087663912","https://openalex.org/W2108706633","https://openalex.org/W2110694683","https://openalex.org/W2132926880","https://openalex.org/W2141059167","https://openalex.org/W2142269152","https://openalex.org/W2142739377","https://openalex.org/W2148146008","https://openalex.org/W2150286046","https://openalex.org/W2154509769","https://openalex.org/W2160303218","https://openalex.org/W2168688111","https://openalex.org/W2170853242","https://openalex.org/W2271914738","https://openalex.org/W2326870000","https://openalex.org/W2334723342","https://openalex.org/W2471645096","https://openalex.org/W2555228033","https://openalex.org/W2615065404","https://openalex.org/W2737196618","https://openalex.org/W2743893844","https://openalex.org/W2779582662","https://openalex.org/W2781173963","https://openalex.org/W2785934310","https://openalex.org/W2885520750","https://openalex.org/W2885694707","https://openalex.org/W2889358860","https://openalex.org/W2898389621","https://openalex.org/W2900127803","https://openalex.org/W2909834406","https://openalex.org/W2947980028","https://openalex.org/W2949949116","https://openalex.org/W2950373774","https://openalex.org/W2952230511","https://openalex.org/W2952607757","https://openalex.org/W2953065444","https://openalex.org/W2953258522","https://openalex.org/W2963347351","https://openalex.org/W2967717440","https://openalex.org/W2977541300","https://openalex.org/W2979741494","https://openalex.org/W2990906036","https://openalex.org/W2995389725","https://openalex.org/W2995494055","https://openalex.org/W3014571082","https://openalex.org/W3016853422","https://openalex.org/W3024570138","https://openalex.org/W3042452836","https://openalex.org/W3042910002","https://openalex.org/W3111171798","https://openalex.org/W3122375914","https://openalex.org/W3128687311","https://openalex.org/W3136918052","https://openalex.org/W3159316433","https://openalex.org/W3198814330","https://openalex.org/W4220655797","https://openalex.org/W4225758372","https://openalex.org/W4286251201","https://openalex.org/W4303699434","https://openalex.org/W4313453841","https://openalex.org/W6683738474","https://openalex.org/W6753075380","https://openalex.org/W6775886142"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W972276598","https://openalex.org/W4246352526","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W2087343574","https://openalex.org/W2121910908"],"abstract_inverted_index":{"Human":[0],"leukocyte":[1],"antigen":[2],"class":[3],"I":[4],"(HLA-I)":[5],"molecules":[6,32],"bind":[7,30],"intracellular":[8],"peptides":[9,28],"produced":[10],"by":[11,134],"protein":[12],"hydrolysis":[13],"and":[14,24,62,73,103,194,200,220],"present":[15],"them":[16,161],"to":[17,99,206,209,224],"the":[18,69,115,118,171,176,179,207,211,222],"T":[19],"cells":[20],"for":[21,81,187,215,221],"immune":[22],"recognition":[23],"response.":[25],"Prediction":[26],"of":[27,41,55,68,90,97,114,117,160,170,178,191],"that":[29,123,137,139,158],"HLA-I":[31],"is":[33,162],"very":[34],"important":[35],"in":[36,47],"immunotherapy.":[37],"A":[38],"growing":[39],"number":[40],"computational":[42],"predictors":[43],"have":[44],"been":[45],"developed":[46],"recent":[48],"years.":[49],"We":[50,85,105,165],"survey":[51],"a":[52,87,167,216],"comprehensive":[53,168],"collection":[54],"27":[56],"tools":[57,214],"focusing":[58],"on":[59,112,196],"their":[60,74,140],"input":[61],"output":[63],"data":[64,101,119],"characteristics,":[65],"key":[66],"aspects":[67,92],"underlying":[70],"predictive":[71,79,141,192],"models":[72,142],"availability.":[75],"Moreover,":[76],"we":[77,156],"evaluate":[78],"performance":[80,193],"eight":[82],"representative":[83],"predictors.":[84],"consider":[86],"wide":[88],"spectrum":[89],"relevant":[91],"including":[93],"allele-specific":[94],"analysis,":[95],"influence":[96],"negative":[98],"positive":[100],"ratios":[102],"runtime.":[104,197],"also":[106],"curate":[107],"high-quality":[108],"benchmark":[109],"datasets":[110],"based":[111],"analysis":[113,136,202],"consistency":[116],"labels.":[120],"Results":[121],"reveal":[122],"each":[124],"considered":[125],"method":[126],"provides":[127,203],"accurate":[128,153],"results,":[129],"which":[130],"can":[131],"be":[132],"explained":[133],"our":[135],"finds":[138],"capture":[143],"meaningful":[144],"binding":[145],"motifs.":[146],"Although":[147],"some":[148],"methods":[149,180],"are":[150],"overall":[151],"more":[152],"than":[154],"others,":[155],"find":[157],"none":[159],"universally":[163],"superior.":[164],"provide":[166],"comparison":[169],"convenience":[172],"as":[173,175,186],"well":[174],"accuracy":[177],"under":[181],"specific":[182,188],"prediction":[183,218],"scenarios,":[184],"such":[185],"alleles,":[189],"metrics":[190],"constraints":[195],"Our":[198],"systematic":[199],"broad":[201],"informative":[204],"clues":[205],"users":[208],"identify":[210],"most":[212],"suitable":[213],"given":[217],"scenario":[219],"developers":[223],"design":[225],"future":[226],"methods.":[227]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
