{"id":"https://openalex.org/W2114970943","doi":"https://doi.org/10.1093/bib/bbr060","title":"Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools","display_name":"Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools","publication_year":2011,"publication_date":"2011-09-22","ids":{"openalex":"https://openalex.org/W2114970943","doi":"https://doi.org/10.1093/bib/bbr060","mag":"2114970943","pmid":"https://pubmed.ncbi.nlm.nih.gov/21949215"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbr060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr060","pdf_url":"https://academic.oup.com/bib/article-pdf/13/3/350/682012/bbr060.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":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/13/3/350/682012/bbr060.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100434028","display_name":"Lei Zhang","orcid":"https://orcid.org/0000-0003-2343-084X"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"L. Zhang","raw_affiliation_strings":["School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China","School of Computer Science, and Shanghai Key Lab of Intelligent Information Processing Fudan University, Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"School of Computer Science, and Shanghai Key Lab of Intelligent Information Processing Fudan University, Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090583271","display_name":"Keiko Udaka","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"K. Udaka","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059001924","display_name":"Hiroshi Mamitsuka","orcid":"https://orcid.org/0000-0002-6607-5617"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"H. Mamitsuka","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5045866167","display_name":"Shanfeng Zhu","orcid":"https://orcid.org/0000-0002-6067-5312"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"S. Zhu","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100434028"],"corresponding_institution_ids":["https://openalex.org/I24943067"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.2572,"has_fulltext":false,"cited_by_count":145,"citation_normalized_percentile":{"value":0.92817872,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"13","issue":"3","first_page":"350","last_page":"364"},"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":0.9993000030517578,"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":0.9988999962806702,"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/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.8269909024238586},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6344574689865112},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.5452426671981812},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5071802139282227},{"id":"https://openalex.org/keywords/mhc-class-i","display_name":"MHC class I","score":0.48927685618400574},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.420812726020813},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.418678343296051},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.36548101902008057},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.3058127164840698},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2630915641784668},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.07979846000671387}],"concepts":[{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.8269909024238586},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6344574689865112},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.5452426671981812},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5071802139282227},{"id":"https://openalex.org/C170627219","wikidata":"https://www.wikidata.org/wiki/Q13218497","display_name":"MHC class I","level":4,"score":0.48927685618400574},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.420812726020813},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.418678343296051},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.36548101902008057},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.3058127164840698},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2630915641784668},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.07979846000671387}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008285","descriptor_name":"Major Histocompatibility Complex","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008285","descriptor_name":"Major Histocompatibility Complex","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008285","descriptor_name":"Major Histocompatibility Complex","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbr060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr060","pdf_url":"https://academic.oup.com/bib/article-pdf/13/3/350/682012/bbr060.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:21949215","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21949215","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/bbr060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr060","pdf_url":"https://academic.oup.com/bib/article-pdf/13/3/350/682012/bbr060.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":[{"score":0.47999998927116394,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2114970943.pdf","grobid_xml":"https://content.openalex.org/works/W2114970943.grobid-xml"},"referenced_works_count":73,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1558421445","https://openalex.org/W1595314835","https://openalex.org/W1974890764","https://openalex.org/W1976311337","https://openalex.org/W1990305601","https://openalex.org/W1990395260","https://openalex.org/W1990748933","https://openalex.org/W1991036680","https://openalex.org/W1993772622","https://openalex.org/W1994048581","https://openalex.org/W2003652884","https://openalex.org/W2006877285","https://openalex.org/W2012385803","https://openalex.org/W2012625502","https://openalex.org/W2020564539","https://openalex.org/W2026272191","https://openalex.org/W2028147409","https://openalex.org/W2028339001","https://openalex.org/W2034694458","https://openalex.org/W2035144728","https://openalex.org/W2047544230","https://openalex.org/W2052321000","https://openalex.org/W2053843590","https://openalex.org/W2055132429","https://openalex.org/W2059874211","https://openalex.org/W2061272711","https://openalex.org/W2067504188","https://openalex.org/W2070639360","https://openalex.org/W2076639605","https://openalex.org/W2077480262","https://openalex.org/W2083900229","https://openalex.org/W2087663912","https://openalex.org/W2094706980","https://openalex.org/W2097283546","https://openalex.org/W2097398162","https://openalex.org/W2098583514","https://openalex.org/W2099500226","https://openalex.org/W2100350770","https://openalex.org/W2100549317","https://openalex.org/W2109086160","https://openalex.org/W2110574412","https://openalex.org/W2110694683","https://openalex.org/W2111066113","https://openalex.org/W2115280552","https://openalex.org/W2117333383","https://openalex.org/W2120399005","https://openalex.org/W2122779464","https://openalex.org/W2125644345","https://openalex.org/W2125732073","https://openalex.org/W2129612249","https://openalex.org/W2130354820","https://openalex.org/W2134378878","https://openalex.org/W2142269152","https://openalex.org/W2142636897","https://openalex.org/W2142739377","https://openalex.org/W2142774061","https://openalex.org/W2144612215","https://openalex.org/W2149350146","https://openalex.org/W2153844761","https://openalex.org/W2160303218","https://openalex.org/W2161062388","https://openalex.org/W2165381821","https://openalex.org/W2168688111","https://openalex.org/W2168749806","https://openalex.org/W2169628767","https://openalex.org/W2432517183","https://openalex.org/W2476598722","https://openalex.org/W2478720029","https://openalex.org/W2796837256","https://openalex.org/W3143486655","https://openalex.org/W4211054902","https://openalex.org/W4239551491"],"related_works":["https://openalex.org/W1840653008","https://openalex.org/W2977793531","https://openalex.org/W2023967363","https://openalex.org/W1939527068","https://openalex.org/W2150433660","https://openalex.org/W2126139339","https://openalex.org/W2168688111","https://openalex.org/W2070684866","https://openalex.org/W4281625971","https://openalex.org/W2134517286"],"abstract_inverted_index":{"Binding":[0],"of":[1,21,25,32,39,53,71,93,98,106,126,133,153,165],"short":[2],"antigenic":[3],"peptides":[4,23,73,104],"to":[5,44,75,176],"major":[6],"histocompatibility":[7],"complex":[8],"(MHC)":[9],"molecules":[10],"is":[11,24,57],"a":[12,150],"core":[13],"step":[14],"in":[15,129],"adaptive":[16],"immune":[17,33],"response.":[18],"Precise":[19],"identification":[20],"MHC-restricted":[22],"great":[26],"significance":[27],"for":[28,63,180],"understanding":[29],"the":[30,37,45,69,124,157,173],"mechanism":[31],"response":[34],"and":[35,50,131,143,159],"promoting":[36],"discovery":[38],"immunogenic":[40],"epitopes.":[41],"However,":[42],"due":[43],"extremely":[46],"high":[47],"MHC":[48,65,77],"polymorphism":[49],"huge":[51],"cost":[52],"biochemical":[54],"experiments,":[55],"there":[56],"no":[58,116],"experimentally":[59,94],"measured":[60],"binding":[61,74,96,103,182],"data":[62,97],"most":[64],"molecules.":[66],"To":[67,122],"address":[68],"problem":[70],"predicting":[72],"these":[76,109],"molecules,":[78],"recently":[79],"computational":[80],"approaches,":[81],"called":[82],"pan-specific":[83,134,141,154,178],"methods,":[84,135],"have":[85],"received":[86],"keen":[87],"interest.":[88],"Pan-specific":[89],"methods":[90,142,179],"make":[91],"use":[92],"obtained":[95],"multiple":[99],"alleles,":[100],"by":[101],"which":[102],"(binders)":[105],"not":[107],"only":[108],"alleles":[110,114],"but":[111],"also":[112],"those":[113],"with":[115],"known":[117],"binders":[118],"can":[119],"be":[120],"predicted.":[121],"investigate":[123],"possibility":[125],"further":[127],"improvement":[128],"performance":[130,160],"usability":[132],"this":[136],"article":[137],"extensively":[138],"reviews":[139],"existing":[140],"their":[144],"web":[145,166],"servers.":[146],"We":[147],"first":[148],"present":[149],"general":[151],"framework":[152],"methods.":[155],"Then,":[156],"strategies":[158],"as":[161,163],"well":[162],"utilities":[164],"servers":[167],"are":[168],"compared.":[169],"Finally,":[170],"we":[171],"discuss":[172],"future":[174],"direction":[175],"improve":[177],"MHC-peptide":[181],"prediction.":[183]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":19},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":12},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":12},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":4}],"updated_date":"2026-02-25T23:00:34.991745","created_date":"2025-10-10T00:00:00"}
