{"id":"https://openalex.org/W4382502864","doi":"https://doi.org/10.1093/bioinformatics/btad392","title":"Understanding the complementarity and plasticity of antibody\u2013antigen interfaces","display_name":"Understanding the complementarity and plasticity of antibody\u2013antigen interfaces","publication_year":2023,"publication_date":"2023-06-29","ids":{"openalex":"https://openalex.org/W4382502864","doi":"https://doi.org/10.1093/bioinformatics/btad392"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad392","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad392","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad392/50739843/btad392.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad392/50739843/btad392.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076251011","display_name":"Yoochan Myung","orcid":"https://orcid.org/0000-0002-6763-9808"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Yoochan Myung","raw_affiliation_strings":["Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute , Melbourne, VIC 3044, Australia","School of Chemistry and Molecular Biosciences, University of Queensland , St Lucia, QLD 4072, Australia","Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne , Melbourne, VIC 3010, Australia","Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne, VIC 3052, Australia"],"affiliations":[{"raw_affiliation_string":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute , Melbourne, VIC 3044, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"School of Chemistry and Molecular Biosciences, University of Queensland , St Lucia, QLD 4072, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne , Melbourne, VIC 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne, VIC 3052, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071950872","display_name":"Douglas E. V. Pires","orcid":"https://orcid.org/0000-0002-3004-2119"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Douglas E V Pires","raw_affiliation_strings":["Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute , Melbourne, VIC 3044, Australia","School of Computing and Information Systems, University of Melbourne , Melbourne, VIC 3010, Australia","Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne, VIC 3052, Australia"],"affiliations":[{"raw_affiliation_string":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute , Melbourne, VIC 3044, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"School of Computing and Information Systems, University of Melbourne , Melbourne, VIC 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne, VIC 3052, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091903225","display_name":"David B. Ascher","orcid":"https://orcid.org/0000-0003-2948-2413"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"David B Ascher","raw_affiliation_strings":["Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute , Melbourne, VIC 3044, Australia","School of Chemistry and Molecular Biosciences, University of Queensland , St Lucia, QLD 4072, Australia","Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne , Melbourne, VIC 3010, Australia","Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne, VIC 3052, Australia"],"affiliations":[{"raw_affiliation_string":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute , Melbourne, VIC 3044, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"School of Chemistry and Molecular Biosciences, University of Queensland , St Lucia, QLD 4072, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne , Melbourne, VIC 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne, VIC 3052, Australia","institution_ids":["https://openalex.org/I165779595"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5076251011"],"corresponding_institution_ids":["https://openalex.org/I142471025","https://openalex.org/I165143802","https://openalex.org/I165779595"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.3138,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.94730193,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"39","issue":"7","first_page":null,"last_page":null},"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/T11124","display_name":"Protein purification and stability","score":0.9986000061035156,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9937000274658203,"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/complementarity","display_name":"Complementarity (molecular biology)","score":0.8007857203483582},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5385900735855103},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.4794520437717438},{"id":"https://openalex.org/keywords/plasticity","display_name":"Plasticity","score":0.42276620864868164},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.4103270173072815},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40848344564437866},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3000447154045105},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.22669872641563416},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18743589520454407},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.10483574867248535}],"concepts":[{"id":"https://openalex.org/C202269582","wikidata":"https://www.wikidata.org/wiki/Q2644277","display_name":"Complementarity (molecular biology)","level":2,"score":0.8007857203483582},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5385900735855103},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.4794520437717438},{"id":"https://openalex.org/C79186407","wikidata":"https://www.wikidata.org/wiki/Q472074","display_name":"Plasticity","level":2,"score":0.42276620864868164},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.4103270173072815},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40848344564437866},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3000447154045105},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.22669872641563416},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18743589520454407},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.10483574867248535},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btad392","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad392","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad392/50739843/btad392.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10329492","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10329492","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10329492/pdf/btad392.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad392","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad392","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad392/50739843/btad392.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1187375252","display_name":null,"funder_award_id":"1174405","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G6454673195","display_name":null,"funder_award_id":"GNT1174405","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320322858","display_name":"State Government of Victoria","ror":"https://ror.org/02xvc5r05"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4382502864.pdf"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1990159344","https://openalex.org/W1997875463","https://openalex.org/W1998063251","https://openalex.org/W1999866186","https://openalex.org/W2002449583","https://openalex.org/W2020972820","https://openalex.org/W2037042031","https://openalex.org/W2063725620","https://openalex.org/W2072854137","https://openalex.org/W2106380530","https://openalex.org/W2110036226","https://openalex.org/W2110505462","https://openalex.org/W2132514101","https://openalex.org/W2151197219","https://openalex.org/W2151445960","https://openalex.org/W2163065611","https://openalex.org/W2169610187","https://openalex.org/W2170110204","https://openalex.org/W2170747616","https://openalex.org/W2253581743","https://openalex.org/W2267291411","https://openalex.org/W2326365831","https://openalex.org/W2400041270","https://openalex.org/W2560264526","https://openalex.org/W2619511074","https://openalex.org/W2625052417","https://openalex.org/W2900437486","https://openalex.org/W2980372463","https://openalex.org/W2991236694","https://openalex.org/W3026328277","https://openalex.org/W3042291772","https://openalex.org/W4213085061","https://openalex.org/W4226091362"],"related_works":["https://openalex.org/W2521519254","https://openalex.org/W3139833644","https://openalex.org/W3123110765","https://openalex.org/W2016937053","https://openalex.org/W4383553409","https://openalex.org/W2212953222","https://openalex.org/W2104948296","https://openalex.org/W1735800226","https://openalex.org/W4285172739","https://openalex.org/W3123208392"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"While":[2],"antibodies":[3,149],"have":[4,36],"been":[5],"ground-breaking":[6],"therapeutic":[7],"agents,":[8],"the":[9,25,38,46,78,117,128,134],"structural":[10,39,47],"determinants":[11,48],"for":[12,102],"antibody":[13,118,129],"binding":[14,131],"specificity":[15],"remain":[16],"to":[17,44,111,113,143,154],"be":[18,151],"fully":[19],"elucidated,":[20],"which":[21,140],"is":[22],"compounded":[23],"by":[24,52],"virtually":[26],"unlimited":[27],"repertoire":[28],"of":[29,41,75,81,116,136,147],"antigens":[30,108],"they":[31],"can":[32,150],"recognize.":[33],"Here,":[34],"we":[35],"explored":[37],"landscapes":[40],"antibody\u2013antigen":[42,137],"interfaces":[43],"identify":[45],"driving":[49],"target":[50,155],"recognition":[51],"assessing":[53],"concavity":[54,66],"and":[55,133,162,166],"interatomic":[56],"interactions.":[57],"Results":[58],"We":[59],"found":[60,88],"that":[61],"complementarity-determining":[62,90],"regions":[63],"utilized":[64,109],"deeper":[65,94,114],"with":[67],"their":[68],"longer":[69],"H3":[70,73],"loops,":[71],"especially":[72,96],"loops":[74],"nanobody":[76],"showing":[77],"deepest":[79],"use":[80],"concavity.":[82],"Of":[83],"all":[84],"amino":[85],"acid":[86],"residues":[87],"in":[89,97,125],"regions,":[91],"tryptophan":[92],"used":[93],"concavity,":[95],"nanobodies,":[98],"making":[99],"it":[100],"suitable":[101],"leveraging":[103],"concave":[104],"antigen":[105,159],"surfaces.":[106,160],"Similarly,":[107],"arginine":[110],"bind":[112],"pockets":[115],"surface.":[119],"Our":[120],"findings":[121],"fill":[122],"a":[123,144],"gap":[124],"knowledge":[126],"about":[127],"specificity,":[130],"affinity,":[132],"nature":[135],"interface":[138],"features,":[139],"will":[141],"lead":[142],"better":[145],"understanding":[146],"how":[148],"more":[152],"effective":[153],"druggable":[156],"sites":[157],"on":[158],"Availability":[161],"implementation":[163],"The":[164],"data":[165],"scripts":[167],"are":[168],"available":[169],"at:":[170],"https://github.com/YoochanMyung/scripts.":[171]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":9}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}