{"id":"https://openalex.org/W4392108614","doi":"https://doi.org/10.3389/fbinf.2024.1295972","title":"Computational identification of antibody-binding epitopes from mimotope datasets","display_name":"Computational identification of antibody-binding epitopes from mimotope datasets","publication_year":2024,"publication_date":"2024-02-22","ids":{"openalex":"https://openalex.org/W4392108614","doi":"https://doi.org/10.3389/fbinf.2024.1295972","pmid":"https://pubmed.ncbi.nlm.nih.gov/38463209"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2024.1295972","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1295972","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2024.1295972/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2024.1295972/pdf?isPublishedV2=False","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101730496","display_name":"Rang Li","orcid":"https://orcid.org/0000-0003-2029-4838"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rang Li","raw_affiliation_strings":["Department of Biomedical Engineering, Boston University, Boston, MA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Boston University, Boston, MA, United States","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093518928","display_name":"Sabrina Wilderotter","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sabrina Wilderotter","raw_affiliation_strings":["Department of Biomedical Engineering, Boston University, Boston, MA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Boston University, Boston, MA, United States","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058738104","display_name":"Madison Stoddard","orcid":"https://orcid.org/0000-0001-9853-8500"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Madison Stoddard","raw_affiliation_strings":["Fractal Therapeutics Inc., Cambridge, MA, United States"],"affiliations":[{"raw_affiliation_string":"Fractal Therapeutics Inc., Cambridge, MA, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050435547","display_name":"Debra Van Egeren","orcid":"https://orcid.org/0000-0002-4017-0413"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Debra Van Egeren","raw_affiliation_strings":["Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, United States"],"affiliations":[{"raw_affiliation_string":"Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, United States","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003610011","display_name":"Arijit Chakravarty","orcid":"https://orcid.org/0000-0003-1338-5432"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Arijit Chakravarty","raw_affiliation_strings":["Fractal Therapeutics Inc., Cambridge, MA, United States"],"affiliations":[{"raw_affiliation_string":"Fractal Therapeutics Inc., Cambridge, MA, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066868698","display_name":"Diane Joseph\u2010McCarthy","orcid":"https://orcid.org/0000-0001-9685-6177"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Diane Joseph-McCarthy","raw_affiliation_strings":["Department of Biomedical Engineering, Boston University, Boston, MA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Boston University, Boston, MA, United States","institution_ids":["https://openalex.org/I111088046"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5066868698"],"corresponding_institution_ids":["https://openalex.org/I111088046"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.838,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.7113808,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"4","issue":null,"first_page":"1295972","last_page":"1295972"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":1.0,"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"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":1.0,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9998999834060669,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9997000098228455,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.9797608852386475},{"id":"https://openalex.org/keywords/mimotope","display_name":"Mimotope","score":0.9476274251937866},{"id":"https://openalex.org/keywords/linear-epitope","display_name":"Linear epitope","score":0.6524650454521179},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6403778195381165},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.6164608597755432},{"id":"https://openalex.org/keywords/conformational-epitope","display_name":"Conformational epitope","score":0.6118669509887695},{"id":"https://openalex.org/keywords/monoclonal-antibody","display_name":"Monoclonal antibody","score":0.5485658049583435},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.5270809531211853},{"id":"https://openalex.org/keywords/phage-display","display_name":"Phage display","score":0.5263903141021729},{"id":"https://openalex.org/keywords/epitope-mapping","display_name":"Epitope mapping","score":0.5021989345550537},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.48213645815849304},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3750734329223633},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.33846205472946167},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.22464659810066223},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15098926424980164}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.9797608852386475},{"id":"https://openalex.org/C9365378","wikidata":"https://www.wikidata.org/wiki/Q426454","display_name":"Mimotope","level":4,"score":0.9476274251937866},{"id":"https://openalex.org/C78598654","wikidata":"https://www.wikidata.org/wiki/Q17140316","display_name":"Linear epitope","level":4,"score":0.6524650454521179},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6403778195381165},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.6164608597755432},{"id":"https://openalex.org/C2780632150","wikidata":"https://www.wikidata.org/wiki/Q5160267","display_name":"Conformational epitope","level":4,"score":0.6118669509887695},{"id":"https://openalex.org/C542903549","wikidata":"https://www.wikidata.org/wiki/Q422248","display_name":"Monoclonal antibody","level":3,"score":0.5485658049583435},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.5270809531211853},{"id":"https://openalex.org/C186268636","wikidata":"https://www.wikidata.org/wiki/Q896217","display_name":"Phage display","level":3,"score":0.5263903141021729},{"id":"https://openalex.org/C2781241564","wikidata":"https://www.wikidata.org/wiki/Q1347450","display_name":"Epitope mapping","level":4,"score":0.5021989345550537},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.48213645815849304},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3750734329223633},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33846205472946167},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.22464659810066223},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15098926424980164},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3389/fbinf.2024.1295972","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1295972","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2024.1295972/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38463209","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38463209","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:null:2144/48822","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pubmed/38463209","pdf_url":null,"source":{"id":"https://openalex.org/S4306402384","display_name":"OpenBU (Boston University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I111088046","host_organization_name":"Boston University","host_organization_lineage":["https://openalex.org/I111088046"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10920257","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10920257","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10920257/pdf/fbinf-04-1295972.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:ea77786d346d4f2ba5cfe2a0a4f4dcb1","is_oa":true,"landing_page_url":"https://doaj.org/article/ea77786d346d4f2ba5cfe2a0a4f4dcb1","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 4 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2024.1295972","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1295972","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2024.1295972/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7300000190734863,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392108614.pdf"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W62276193","https://openalex.org/W1548632952","https://openalex.org/W1559661072","https://openalex.org/W1891870091","https://openalex.org/W1965173570","https://openalex.org/W1966109425","https://openalex.org/W1968643522","https://openalex.org/W1972242350","https://openalex.org/W1976801077","https://openalex.org/W1981284849","https://openalex.org/W1982329322","https://openalex.org/W1983721404","https://openalex.org/W1985799231","https://openalex.org/W1989375126","https://openalex.org/W2001896084","https://openalex.org/W2007282352","https://openalex.org/W2007402644","https://openalex.org/W2013652077","https://openalex.org/W2017205210","https://openalex.org/W2017956110","https://openalex.org/W2024651005","https://openalex.org/W2037263319","https://openalex.org/W2042492527","https://openalex.org/W2043449832","https://openalex.org/W2058477978","https://openalex.org/W2061558891","https://openalex.org/W2062204035","https://openalex.org/W2065236789","https://openalex.org/W2068125497","https://openalex.org/W2068265376","https://openalex.org/W2073490027","https://openalex.org/W2083982805","https://openalex.org/W2097508364","https://openalex.org/W2097671323","https://openalex.org/W2099003177","https://openalex.org/W2099427184","https://openalex.org/W2099451628","https://openalex.org/W2103313179","https://openalex.org/W2121477839","https://openalex.org/W2132629607","https://openalex.org/W2133034893","https://openalex.org/W2136130231","https://openalex.org/W2136877202","https://openalex.org/W2141316307","https://openalex.org/W2143210482","https://openalex.org/W2143600397","https://openalex.org/W2276229678","https://openalex.org/W2419493891","https://openalex.org/W2462048418","https://openalex.org/W2521166570","https://openalex.org/W2524428139","https://openalex.org/W2562638954","https://openalex.org/W2777980778","https://openalex.org/W2785498945","https://openalex.org/W4240783332","https://openalex.org/W4295203385","https://openalex.org/W4302367531"],"related_works":["https://openalex.org/W2242496419","https://openalex.org/W2272555026","https://openalex.org/W2049956343","https://openalex.org/W2029633855","https://openalex.org/W2076628539","https://openalex.org/W972031962","https://openalex.org/W2503828389","https://openalex.org/W2141316307","https://openalex.org/W49053791","https://openalex.org/W4289953209"],"abstract_inverted_index":{"<b>Introduction:</b>":[0],"A":[1],"fundamental":[2],"challenge":[3,24],"in":[4,42,135,169,211],"computational":[5],"vaccinology":[6],"is":[7,25,159,215,235],"that":[8,26,53,84,106,165,185],"most":[9,55],"B-cell":[10],"epitopes":[11,120,173],"are":[12,54],"conformational":[13,212,227],"and":[14,144,172,205,246],"therefore":[15],"hard":[16],"to":[17,70,88,100,105,117,155,189,192,195,202],"predict":[18],"from":[19,244],"sequence":[20,34],"alone.":[21],"Another":[22],"significant":[23],"a":[27,36,51,71,129,160,179,183,197,216],"great":[28],"deal":[29],"of":[30,35,50,64,92,110,124,132,138,226],"the":[31,48,62,89,101,122,125,133,136,170,175,190,224,241],"amino":[32],"acid":[33],"viral":[37],"surface":[38,65,123],"protein":[39,52],"might":[40],"not":[41,68,187],"fact":[43],"be":[44,115,209],"antigenic.":[45],"Thus,":[46],"identifying":[47],"regions":[49],"promising":[56],"for":[57,152,167,200,223],"vaccine":[58],"design":[59],"based":[60],"on":[61,121,174],"degree":[63],"exposure":[66],"may":[67,181,207],"lead":[69],"clinically":[72],"relevant":[73,199],"immune":[74],"response.":[75],"<b>Methods:</b>":[76],"Linear":[77],"peptides":[78,113],"selected":[79],"by":[80],"phage":[81],"display":[82],"experiments":[83],"have":[85,96,182],"high":[86],"affinity":[87],"monoclonal":[90],"antibody":[91],"interest":[93],"(\"mimotopes\")":[94],"usually":[95],"similar":[97],"physicochemical":[98],"properties":[99],"antigen":[102,126,134],"epitope":[103,191,219],"corresponding":[104],"antibody.":[107],"The":[108,157,233],"sequences":[109],"these":[111],"linear":[112,231],"can":[114],"used":[116],"find":[118],"possible":[119],"structure":[127],"or":[128],"homology":[130],"model":[131],"absence":[137],"an":[139,203,236],"antigen-antibody":[140],"complex":[141],"structure.":[142],"<b>Results":[143],"Discussion:</b>":[145],"Herein":[146],"we":[147],"describe":[148],"two":[149,247],"novel":[150,161],"methods":[151],"mapping":[153],"mimotopes":[154,171],"epitopes.":[156,213,232],"first":[158],"algorithm":[162,221],"named":[163],"MimoTree":[164,214,245],"allows":[166],"gaps":[168],"antigen.":[176],"More":[177],"specifically,":[178],"mimotope":[180],"gap":[184],"does":[186],"match":[188],"allow":[193],"it":[194],"adopt":[196],"conformation":[198],"binding":[201],"antibody,":[204],"residues":[206],"similarly":[208],"discontinuous":[210],"fully":[217],"automated":[218],"detection":[220],"suitable":[222],"identification":[225],"as":[228,230],"well":[229],"second":[234],"ensemble":[237],"approach,":[238],"which":[239],"combines":[240],"prediction":[242],"results":[243],"existing":[248],"methods.":[249]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-13T16:22:10.518609","created_date":"2025-10-10T00:00:00"}
