{"id":"https://openalex.org/W3004938669","doi":"https://doi.org/10.1109/bibm47256.2019.8983334","title":"A computational framework for deep learning-based epitope prediction by using structure and sequence information","display_name":"A computational framework for deep learning-based epitope prediction by using structure and sequence information","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W3004938669","doi":"https://doi.org/10.1109/bibm47256.2019.8983334","mag":"3004938669"},"language":"en","primary_location":{"id":"doi:10.1109/bibm47256.2019.8983334","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983334","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100327645","display_name":"Younghoon Kim","orcid":"https://orcid.org/0000-0001-7261-3066"},"institutions":[{"id":"https://openalex.org/I878022262","display_name":"Korea Institute of Science & Technology Information","ror":"https://ror.org/01k4yrm29","country_code":"KR","type":"facility","lineage":["https://openalex.org/I2801339556","https://openalex.org/I4210144908","https://openalex.org/I4387152098","https://openalex.org/I878022262"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Younghoon Kim","raw_affiliation_strings":["Center for Supercomputing Applications, KISTI,Daejeon,Rep. Korea","Center for Supercomputing Applications, KISTI, Daejeon, Rep. Korea"],"affiliations":[{"raw_affiliation_string":"Center for Supercomputing Applications, KISTI,Daejeon,Rep. Korea","institution_ids":["https://openalex.org/I878022262"]},{"raw_affiliation_string":"Center for Supercomputing Applications, KISTI, Daejeon, Rep. Korea","institution_ids":["https://openalex.org/I878022262"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069177443","display_name":"Junehawk Lee","orcid":"https://orcid.org/0000-0001-8908-0884"},"institutions":[{"id":"https://openalex.org/I878022262","display_name":"Korea Institute of Science & Technology Information","ror":"https://ror.org/01k4yrm29","country_code":"KR","type":"facility","lineage":["https://openalex.org/I2801339556","https://openalex.org/I4210144908","https://openalex.org/I4387152098","https://openalex.org/I878022262"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Junehawk Lee","raw_affiliation_strings":["Center for Supercomputing Applications, KISTI,Daejeon,Rep. Korea","Center for Supercomputing Applications, KISTI, Daejeon, Rep. Korea"],"affiliations":[{"raw_affiliation_string":"Center for Supercomputing Applications, KISTI,Daejeon,Rep. Korea","institution_ids":["https://openalex.org/I878022262"]},{"raw_affiliation_string":"Center for Supercomputing Applications, KISTI, Daejeon, Rep. Korea","institution_ids":["https://openalex.org/I878022262"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082595926","display_name":"Kyungsoo Ha","orcid":"https://orcid.org/0009-0000-5592-3556"},"institutions":[{"id":"https://openalex.org/I4210155048","display_name":"Osong Medical Innovation Foundation","ror":"https://ror.org/04jr4g753","country_code":"KR","type":"other","lineage":["https://openalex.org/I4210155048"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kyungsoo Ha","raw_affiliation_strings":["New Drug Development Center Kbiohealth,Cheongju-si,Chungbuk,Rep. Korea","New Drug Development Center Kbiohealth, Cheongju-si, Chungbuk, Rep. Korea"],"affiliations":[{"raw_affiliation_string":"New Drug Development Center Kbiohealth,Cheongju-si,Chungbuk,Rep. Korea","institution_ids":["https://openalex.org/I4210155048"]},{"raw_affiliation_string":"New Drug Development Center Kbiohealth, Cheongju-si, Chungbuk, Rep. Korea","institution_ids":["https://openalex.org/I4210155048"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102735368","display_name":"Won\u2010Kyu Lee","orcid":"https://orcid.org/0000-0003-4040-1100"},"institutions":[{"id":"https://openalex.org/I4210155048","display_name":"Osong Medical Innovation Foundation","ror":"https://ror.org/04jr4g753","country_code":"KR","type":"other","lineage":["https://openalex.org/I4210155048"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Won-Kyu Lee","raw_affiliation_strings":["New Drug Development Center Kbiohealth,Cheongju-si,Chungbuk,Rep. Korea","New Drug Development Center Kbiohealth, Cheongju-si, Chungbuk, Rep. Korea"],"affiliations":[{"raw_affiliation_string":"New Drug Development Center Kbiohealth,Cheongju-si,Chungbuk,Rep. Korea","institution_ids":["https://openalex.org/I4210155048"]},{"raw_affiliation_string":"New Drug Development Center Kbiohealth, Cheongju-si, Chungbuk, Rep. Korea","institution_ids":["https://openalex.org/I4210155048"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111822552","display_name":"Deok Rim Heo","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155048","display_name":"Osong Medical Innovation Foundation","ror":"https://ror.org/04jr4g753","country_code":"KR","type":"other","lineage":["https://openalex.org/I4210155048"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Deok Rim Heo","raw_affiliation_strings":["New Drug Development Center Kbiohealth,Cheongju-si,Chungbuk,Rep. Korea","New Drug Development Center Kbiohealth, Cheongju-si, Chungbuk, Rep. Korea"],"affiliations":[{"raw_affiliation_string":"New Drug Development Center Kbiohealth,Cheongju-si,Chungbuk,Rep. Korea","institution_ids":["https://openalex.org/I4210155048"]},{"raw_affiliation_string":"New Drug Development Center Kbiohealth, Cheongju-si, Chungbuk, Rep. Korea","institution_ids":["https://openalex.org/I4210155048"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112070268","display_name":"Ju Rang Woo","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155048","display_name":"Osong Medical Innovation Foundation","ror":"https://ror.org/04jr4g753","country_code":"KR","type":"other","lineage":["https://openalex.org/I4210155048"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Ju Rang Woo","raw_affiliation_strings":["New Drug Development Center Kbiohealth,Cheongju-si,Chungbuk,Rep. Korea","New Drug Development Center Kbiohealth, Cheongju-si, Chungbuk, Rep. Korea"],"affiliations":[{"raw_affiliation_string":"New Drug Development Center Kbiohealth,Cheongju-si,Chungbuk,Rep. Korea","institution_ids":["https://openalex.org/I4210155048"]},{"raw_affiliation_string":"New Drug Development Center Kbiohealth, Cheongju-si, Chungbuk, Rep. Korea","institution_ids":["https://openalex.org/I4210155048"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008207995","display_name":"Seok Jong Yu","orcid":"https://orcid.org/0000-0002-2272-9869"},"institutions":[{"id":"https://openalex.org/I878022262","display_name":"Korea Institute of Science & Technology Information","ror":"https://ror.org/01k4yrm29","country_code":"KR","type":"facility","lineage":["https://openalex.org/I2801339556","https://openalex.org/I4210144908","https://openalex.org/I4387152098","https://openalex.org/I878022262"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Seok Jong Yu","raw_affiliation_strings":["Center for Supercomputing Applications, KISTI,Daejeon,Rep. Korea","Center for Supercomputing Applications, KISTI, Daejeon, Rep. Korea"],"affiliations":[{"raw_affiliation_string":"Center for Supercomputing Applications, KISTI,Daejeon,Rep. Korea","institution_ids":["https://openalex.org/I878022262"]},{"raw_affiliation_string":"Center for Supercomputing Applications, KISTI, Daejeon, Rep. Korea","institution_ids":["https://openalex.org/I878022262"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5100327645"],"corresponding_institution_ids":["https://openalex.org/I878022262"],"apc_list":null,"apc_paid":null,"fwci":0.2557,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.57147957,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"1208","last_page":"1210"},"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9955999851226807,"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"}},{"id":"https://openalex.org/T10580","display_name":"Immunotherapy and Immune Responses","score":0.989799976348877,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.8216526508331299},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.79958176612854},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6357452869415283},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.575239896774292},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.47744041681289673},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47537103295326233},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.466951459646225},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.46455806493759155},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.43604645133018494},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.43318164348602295},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38874945044517517},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.1931357979774475},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.14905381202697754},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1285070776939392}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.8216526508331299},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.79958176612854},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6357452869415283},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.575239896774292},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47744041681289673},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47537103295326233},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.466951459646225},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.46455806493759155},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.43604645133018494},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.43318164348602295},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38874945044517517},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.1931357979774475},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.14905381202697754},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1285070776939392},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm47256.2019.8983334","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983334","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.6299999952316284,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W1501531009","https://openalex.org/W2126396156","https://openalex.org/W2512201206","https://openalex.org/W2743893844","https://openalex.org/W2953065444","https://openalex.org/W2963347351"],"related_works":["https://openalex.org/W2021824670","https://openalex.org/W2009867644","https://openalex.org/W2363997565","https://openalex.org/W1981120125","https://openalex.org/W3036615648","https://openalex.org/W2408448169","https://openalex.org/W2182598264","https://openalex.org/W2075879923","https://openalex.org/W1978626146","https://openalex.org/W2060253881"],"abstract_inverted_index":{"Precise":[0],"prediction":[1,53,68,97,119,137,176,185],"of":[2,15,27,30,37,50,55,83,153,156,169],"the":[3,16,35,48,51,56,100,110,117,150,160,164,170,175,184],"antigens":[4],"that":[5],"bind":[6],"to":[7,94,129,132],"major":[8],"histocompatibility":[9],"complex":[10],"(MHC)":[11],"molecules":[12],"is":[13,92],"one":[14],"most":[17],"important":[18],"steps":[19],"for":[20,34,146],"many":[21],"immune":[22],"response-related":[23],"studies":[24],"including":[25,74],"identification":[26],"neoantigen":[28],"capable":[29],"recognizing":[31],"cancer":[32],"cells":[33],"implementation":[36],"personalized":[38],"immunotherapy":[39],"as":[40,42],"well":[41],"vaccine/therapeutic":[43],"protein":[44,75],"development.":[45],"To":[46],"overcome":[47],"limitations":[49],"limited":[52],"performance":[54,98],"existing":[57],"models,":[58],"we":[59,121],"developed":[60,123],"a":[61,106,124,141,154,188,194],"new":[62,72,90,118],"convolutional":[63],"neural":[64],"network":[65],"(CNN)-based":[66],"epitope":[67,85,136,147],"model":[69,91],"by":[70],"incorporating":[71],"features":[73],"sequence":[76,155,165],"vectors":[77],"(Prot2Vec),":[78],"chemical":[79],"and":[80,86,143,166,182,191],"structural":[81],"characteristics":[82],"an":[84],"MHC":[87,171],"molecule.":[88],"Our":[89],"optimized":[93],"achieve":[95],"better":[96],"than":[99],"conventional":[101],"methods":[102],"when":[103],"validated":[104],"with":[105,116],"benchmark":[107],"dataset":[108],"from":[109],"Immune":[111],"Epitope":[112],"Database":[113],"(IEDB).":[114],"Along":[115],"model,":[120],"also":[122,192],"web-based":[125],"framework,":[126],"called":[127],"Kepre,":[128],"provide":[130],"interfaces":[131],"our":[133],"novel":[134],"CNN-based":[135],"functionalities.":[138],"Kepre":[139,158,173],"provides":[140,183],"user-friendly":[142],"automated":[144],"interface":[145],"prediction.":[148],"Upon":[149],"researcher's":[151],"submission":[152],"interest,":[157],"predicts":[159],"binding":[161],"probability":[162],"between":[163],"each":[167],"type":[168],"molecules.":[172],"runs":[174],"analysis":[177],"on":[178],"high-throughput":[179],"computing":[180],"infrastructure":[181],"results":[186],"in":[187,193],"user-interactable":[189],"GUI":[190],"pdf":[195],"formatted":[196],"report":[197],"file.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2021,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}