{"id":"https://openalex.org/W1979874740","doi":"https://doi.org/10.1093/nar/gkj053","title":"Epitome: database of structure-inferred antigenic epitopes","display_name":"Epitome: database of structure-inferred antigenic epitopes","publication_year":2005,"publication_date":"2005-12-28","ids":{"openalex":"https://openalex.org/W1979874740","doi":"https://doi.org/10.1093/nar/gkj053","mag":"1979874740","pmid":"https://pubmed.ncbi.nlm.nih.gov/16381978"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkj053","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj053","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D777/3924491/gkj053.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D777/3924491/gkj053.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048927341","display_name":"Avner Schlessinger","orcid":"https://orcid.org/0000-0003-4007-7814"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"A. Schlessinger","raw_affiliation_strings":["CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 St Nicholas Avenue, room 804, New York, NY 10032, USA. as2067@columbia.edu","CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 St Nicholas Avenue, room 804, New York, NY 10032, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 St Nicholas Avenue, room 804, New York, NY 10032, USA. as2067@columbia.edu","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 St Nicholas Avenue, room 804, New York, NY 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5048927341"],"corresponding_institution_ids":["https://openalex.org/I78577930"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":4.86,"has_fulltext":true,"cited_by_count":92,"citation_normalized_percentile":{"value":0.94814334,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"34","issue":"90001","first_page":"D777","last_page":"D780"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9997000098228455,"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":0.9997000098228455,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","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":0.9085681438446045},{"id":"https://openalex.org/keywords/epitome","display_name":"Epitome","score":0.871558666229248},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7663344144821167},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.7051380276679993},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.5643770694732666},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3904719948768616},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20421060919761658},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.0780797004699707}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.9085681438446045},{"id":"https://openalex.org/C2775858994","wikidata":"https://www.wikidata.org/wiki/Q5383732","display_name":"Epitome","level":2,"score":0.871558666229248},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7663344144821167},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.7051380276679993},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.5643770694732666},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3904719948768616},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20421060919761658},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.0780797004699707},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001666","descriptor_name":"Binding Sites, Antibody","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001666","descriptor_name":"Binding Sites, Antibody","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001666","descriptor_name":"Binding Sites, Antibody","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018985","descriptor_name":"Epitopes, B-Lymphocyte","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D018985","descriptor_name":"Epitopes, B-Lymphocyte","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D018985","descriptor_name":"Epitopes, B-Lymphocyte","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D018985","descriptor_name":"Epitopes, B-Lymphocyte","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018985","descriptor_name":"Epitopes, B-Lymphocyte","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018985","descriptor_name":"Epitopes, B-Lymphocyte","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","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":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkj053","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj053","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D777/3924491/gkj053.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16381978","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16381978","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.821.8839","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.821.8839","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://nar.oxfordjournals.org/content/34/suppl_1/D777.full.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1347416","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1347416","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkj053","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj053","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D777/3924491/gkj053.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6299999952316284,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1070260364","display_name":null,"funder_award_id":"R01 LM007329","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G1309033093","display_name":null,"funder_award_id":"R01-GM64633-01","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3886416580","display_name":null,"funder_award_id":"R01 GM064633","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4474317619","display_name":null,"funder_award_id":"R01-LM07329-01","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332603","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1979874740.pdf","grobid_xml":"https://content.openalex.org/works/W1979874740.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W564309233","https://openalex.org/W1483944095","https://openalex.org/W1795576732","https://openalex.org/W1933777541","https://openalex.org/W1967965427","https://openalex.org/W1977783553","https://openalex.org/W2008708467","https://openalex.org/W2022231632","https://openalex.org/W2026979552","https://openalex.org/W2031772330","https://openalex.org/W2040074453","https://openalex.org/W2048848017","https://openalex.org/W2074534136","https://openalex.org/W2075770210","https://openalex.org/W2083445427","https://openalex.org/W2085277871","https://openalex.org/W2094148990","https://openalex.org/W2099254366","https://openalex.org/W2101220662","https://openalex.org/W2103675269","https://openalex.org/W2105438341","https://openalex.org/W2106150646","https://openalex.org/W2110036226","https://openalex.org/W2127552260","https://openalex.org/W2130479394","https://openalex.org/W2136525667","https://openalex.org/W2140174199","https://openalex.org/W2143467722","https://openalex.org/W2152326664","https://openalex.org/W2156469184","https://openalex.org/W2158714788","https://openalex.org/W2166233246","https://openalex.org/W2168267323","https://openalex.org/W2171049846","https://openalex.org/W4239198058"],"related_works":["https://openalex.org/W3151712336","https://openalex.org/W1995642259","https://openalex.org/W2051533144","https://openalex.org/W4231592335","https://openalex.org/W564987741","https://openalex.org/W1998990477","https://openalex.org/W3006807070","https://openalex.org/W567380492","https://openalex.org/W2781271814","https://openalex.org/W2205639271"],"abstract_inverted_index":{"Immunoglobulin":[0],"molecules":[1],"specifically":[2],"recognize":[3],"particular":[4],"areas":[5,12],"on":[6,78,93],"the":[7,28,35,52,63,79,94,124,128,159,165],"surface":[8],"of":[9,20,30,51,59,105,141,149,158],"proteins.":[10,146],"These":[11],"are":[13,85,162],"commonly":[14],"dubbed":[15],"B-cell":[16],"epitopes.":[17],"The":[18,180],"identification":[19],"epitopes":[21,38],"in":[22,55,65,145,164],"proteins":[23],"is":[24,62,182],"important":[25],"both":[26],"for":[27,47,109],"design":[29],"experiments":[31],"and":[32,39,69,89,167],"vaccines.":[33],"Additionally,":[34,116],"interactions":[36,61,73,84,126,136],"between":[37,67,86],"antibodies":[40],"have":[41,112],"often":[42],"served":[43],"as":[44],"a":[45,57,87,102,119,139,155],"model":[46],"protein-protein":[48],"interactions.":[49,71],"One":[50],"main":[53],"obstacles":[54],"creating":[56],"database":[58,140,181],"antigen-antibody":[60,130],"difficulty":[64],"distinguishing":[66],"antigenic":[68,125,143],"non-antigenic":[70,83],"Antigenic":[72],"involve":[74],"specific":[75],"recognition":[76],"sites":[77],"antibody's":[80],"surface,":[81],"while":[82],"protein":[88],"any":[90],"other":[91],"site":[92],"antibody.":[95],"To":[96],"solve":[97],"this":[98],"problem,":[99],"we":[100,117],"performed":[101],"comparative":[103],"analysis":[104],"all":[106,150],"protein-antibody":[107],"complexes":[108],"which":[110],"structures":[111],"been":[113],"experimentally":[114],"determined.":[115],"developed":[118],"semi-automated":[120],"tool":[121],"that":[122,161],"identified":[123],"within":[127],"known":[129,151],"complex":[131,153],"structures.":[132],"We":[133],"compiled":[134],"those":[135],"into":[137],"Epitome,":[138],"structure-inferred":[142],"residues":[144,160],"Epitome":[147],"consists":[148],"antigen/antibody":[152],"structures,":[154],"detailed":[156],"description":[157],"involved":[163],"interactions,":[166],"their":[168],"sequence/structure":[169],"environments.":[170],"Interactions":[171],"can":[172],"be":[173],"visualized":[174],"using":[175],"an":[176],"interface":[177],"to":[178],"Jmol.":[179],"available":[183],"at":[184],"http://www.rostlab.org/services/epitome/.":[185]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":4}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}