{"id":"https://openalex.org/W1995468080","doi":"https://doi.org/10.1186/1471-2105-15-77","title":"Predicting HIV-1 broadly neutralizing antibody epitope networks using neutralization titers and a novel computational method","display_name":"Predicting HIV-1 broadly neutralizing antibody epitope networks using neutralization titers and a novel computational method","publication_year":2014,"publication_date":"2014-03-19","ids":{"openalex":"https://openalex.org/W1995468080","doi":"https://doi.org/10.1186/1471-2105-15-77","mag":"1995468080","pmid":"https://pubmed.ncbi.nlm.nih.gov/24646213"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-77","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-77","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-77","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-77","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103569611","display_name":"Mark C. Evans","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Mark C Evans","raw_affiliation_strings":["Monogram Biosciences Inc, 345 Oyster Point Blvd, South San Francisco, CA, 94080, USA","Monogram Biosciences, Inc., South San Francisco, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Monogram Biosciences Inc, 345 Oyster Point Blvd, South San Francisco, CA, 94080, USA","institution_ids":[]},{"raw_affiliation_string":"Monogram Biosciences, Inc., South San Francisco, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069660996","display_name":"Pham Phung","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pham Phung","raw_affiliation_strings":["Monogram Biosciences Inc, 345 Oyster Point Blvd, South San Francisco, CA, 94080, USA","Monogram Biosciences, Inc., South San Francisco, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Monogram Biosciences Inc, 345 Oyster Point Blvd, South San Francisco, CA, 94080, USA","institution_ids":[]},{"raw_affiliation_string":"Monogram Biosciences, Inc., South San Francisco, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025438598","display_name":"Agn\u00e8s Paquet","orcid":"https://orcid.org/0000-0001-8669-1495"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Agnes C Paquet","raw_affiliation_strings":["Monogram Biosciences Inc, 345 Oyster Point Blvd, South San Francisco, CA, 94080, USA","Monogram Biosciences, Inc., South San Francisco, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Monogram Biosciences Inc, 345 Oyster Point Blvd, South San Francisco, CA, 94080, USA","institution_ids":[]},{"raw_affiliation_string":"Monogram Biosciences, Inc., South San Francisco, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007773459","display_name":"Anvi Parikh","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Anvi Parikh","raw_affiliation_strings":["Monogram Biosciences Inc, 345 Oyster Point Blvd, South San Francisco, CA, 94080, USA","Monogram Biosciences, Inc., South San Francisco, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Monogram Biosciences Inc, 345 Oyster Point Blvd, South San Francisco, CA, 94080, USA","institution_ids":[]},{"raw_affiliation_string":"Monogram Biosciences, Inc., South San Francisco, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042931433","display_name":"Christos J. Petropoulos","orcid":"https://orcid.org/0000-0001-5496-8090"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Christos J Petropoulos","raw_affiliation_strings":["Monogram Biosciences Inc, 345 Oyster Point Blvd, South San Francisco, CA, 94080, USA","Monogram Biosciences, Inc., South San Francisco, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Monogram Biosciences Inc, 345 Oyster Point Blvd, South San Francisco, CA, 94080, USA","institution_ids":[]},{"raw_affiliation_string":"Monogram Biosciences, Inc., South San Francisco, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034553895","display_name":"Terri Wrin","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Terri Wrin","raw_affiliation_strings":["Monogram Biosciences Inc, 345 Oyster Point Blvd, South San Francisco, CA, 94080, USA","Monogram Biosciences, Inc., South San Francisco, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Monogram Biosciences Inc, 345 Oyster Point Blvd, South San Francisco, CA, 94080, USA","institution_ids":[]},{"raw_affiliation_string":"Monogram Biosciences, Inc., South San Francisco, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063681285","display_name":"Mojgan Haddad","orcid":null},"institutions":[{"id":"https://openalex.org/I1325784139","display_name":"Yahoo (United Kingdom)","ror":"https://ror.org/038p3gq39","country_code":"GB","type":"company","lineage":["https://openalex.org/I1325784139","https://openalex.org/I4210134091"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mojgan Haddad","raw_affiliation_strings":["Monogram Biosciences Inc,, 345 Oyster Point Blvd,, South San Francisco, CA 94080, USA. mojganhd@yahoo.com","Monogram Biosciences, Inc., South San Francisco, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Monogram Biosciences Inc,, 345 Oyster Point Blvd,, South San Francisco, CA 94080, USA. mojganhd@yahoo.com","institution_ids":["https://openalex.org/I1325784139"]},{"raw_affiliation_string":"Monogram Biosciences, Inc., South San Francisco, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5103569611"],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5691,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.66241063,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"15","issue":"1","first_page":"77","last_page":"77"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.8844000101089478,"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":0.8844000101089478,"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/T10112","display_name":"HIV Research and Treatment","score":0.06949999928474426,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"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":0.00989999994635582,"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/epitope","display_name":"Epitope","score":0.9371581077575684},{"id":"https://openalex.org/keywords/neutralization","display_name":"Neutralization","score":0.8834735155105591},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.6637094020843506},{"id":"https://openalex.org/keywords/neutralizing-antibody","display_name":"Neutralizing antibody","score":0.6342145800590515},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.5615050792694092},{"id":"https://openalex.org/keywords/monoclonal-antibody","display_name":"Monoclonal antibody","score":0.556921124458313},{"id":"https://openalex.org/keywords/epitope-mapping","display_name":"Epitope mapping","score":0.5093799829483032},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.47574540972709656},{"id":"https://openalex.org/keywords/linear-epitope","display_name":"Linear epitope","score":0.45742523670196533},{"id":"https://openalex.org/keywords/titer","display_name":"Titer","score":0.4333764612674713},{"id":"https://openalex.org/keywords/viral-envelope","display_name":"Viral envelope","score":0.43033555150032043},{"id":"https://openalex.org/keywords/hiv-vaccine","display_name":"HIV vaccine","score":0.4135872423648834},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.2606905996799469},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.22488486766815186},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17348748445510864},{"id":"https://openalex.org/keywords/vaccine-trial","display_name":"Vaccine trial","score":0.12300571799278259}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.9371581077575684},{"id":"https://openalex.org/C14086860","wikidata":"https://www.wikidata.org/wiki/Q337120","display_name":"Neutralization","level":3,"score":0.8834735155105591},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.6637094020843506},{"id":"https://openalex.org/C2779261636","wikidata":"https://www.wikidata.org/wiki/Q7003054","display_name":"Neutralizing antibody","level":3,"score":0.6342145800590515},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.5615050792694092},{"id":"https://openalex.org/C542903549","wikidata":"https://www.wikidata.org/wiki/Q422248","display_name":"Monoclonal antibody","level":3,"score":0.556921124458313},{"id":"https://openalex.org/C2781241564","wikidata":"https://www.wikidata.org/wiki/Q1347450","display_name":"Epitope mapping","level":4,"score":0.5093799829483032},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47574540972709656},{"id":"https://openalex.org/C78598654","wikidata":"https://www.wikidata.org/wiki/Q17140316","display_name":"Linear epitope","level":4,"score":0.45742523670196533},{"id":"https://openalex.org/C32611913","wikidata":"https://www.wikidata.org/wiki/Q2166189","display_name":"Titer","level":3,"score":0.4333764612674713},{"id":"https://openalex.org/C97380033","wikidata":"https://www.wikidata.org/wiki/Q994215","display_name":"Viral envelope","level":3,"score":0.43033555150032043},{"id":"https://openalex.org/C2780195530","wikidata":"https://www.wikidata.org/wiki/Q1479804","display_name":"HIV vaccine","level":4,"score":0.4135872423648834},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.2606905996799469},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.22488486766815186},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17348748445510864},{"id":"https://openalex.org/C2778190748","wikidata":"https://www.wikidata.org/wiki/Q7907956","display_name":"Vaccine trial","level":3,"score":0.12300571799278259}],"mesh":[{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001666","descriptor_name":"Binding Sites, Antibody","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001666","descriptor_name":"Binding Sites, Antibody","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001666","descriptor_name":"Binding Sites, Antibody","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001666","descriptor_name":"Binding Sites, Antibody","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001666","descriptor_name":"Binding Sites, Antibody","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001666","descriptor_name":"Binding Sites, Antibody","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009500","descriptor_name":"Neutralization Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009500","descriptor_name":"Neutralization Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009500","descriptor_name":"Neutralization Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015483","descriptor_name":"HIV Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-15-77","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-77","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-77","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24646213","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24646213","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2991699","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3999910","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3999910","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3999910","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-77","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-77","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-77","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8199999928474426,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306138","display_name":"International AIDS Vaccine Initiative","ror":"https://ror.org/05ayv2203"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332622","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1995468080.pdf","grobid_xml":"https://content.openalex.org/works/W1995468080.grobid-xml"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W86473820","https://openalex.org/W1969761972","https://openalex.org/W1971233211","https://openalex.org/W1982490791","https://openalex.org/W1982633968","https://openalex.org/W1983113740","https://openalex.org/W1984695931","https://openalex.org/W1985204165","https://openalex.org/W1990675829","https://openalex.org/W1992888167","https://openalex.org/W1997677784","https://openalex.org/W2004360551","https://openalex.org/W2008708467","https://openalex.org/W2020736655","https://openalex.org/W2034160159","https://openalex.org/W2038633253","https://openalex.org/W2039388179","https://openalex.org/W2040074453","https://openalex.org/W2042975711","https://openalex.org/W2052937459","https://openalex.org/W2056710036","https://openalex.org/W2058632331","https://openalex.org/W2070220357","https://openalex.org/W2072675037","https://openalex.org/W2083726777","https://openalex.org/W2087197916","https://openalex.org/W2089615515","https://openalex.org/W2094750078","https://openalex.org/W2098037300","https://openalex.org/W2099427184","https://openalex.org/W2102254707","https://openalex.org/W2103053267","https://openalex.org/W2103313179","https://openalex.org/W2103712192","https://openalex.org/W2106228977","https://openalex.org/W2113236498","https://openalex.org/W2120653364","https://openalex.org/W2121477839","https://openalex.org/W2122617162","https://openalex.org/W2122854841","https://openalex.org/W2125866257","https://openalex.org/W2132629607","https://openalex.org/W2132660391","https://openalex.org/W2133034893","https://openalex.org/W2135151522","https://openalex.org/W2137015675","https://openalex.org/W2142072041","https://openalex.org/W2149509877","https://openalex.org/W2150537020","https://openalex.org/W2151445960","https://openalex.org/W2152640863","https://openalex.org/W2157210912","https://openalex.org/W2157576293","https://openalex.org/W2240372320","https://openalex.org/W2320964921","https://openalex.org/W3147254695","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W4392361461","https://openalex.org/W4236556026","https://openalex.org/W3096915742","https://openalex.org/W1540778049","https://openalex.org/W3189724180","https://openalex.org/W4283585174","https://openalex.org/W2015286028","https://openalex.org/W4231564783","https://openalex.org/W2062700146","https://openalex.org/W4241031629"],"abstract_inverted_index":{"BACKGROUND:":[0],"Recent":[1],"efforts":[2],"in":[3,87,229,278],"HIV-1":[4,83,291],"vaccine":[5],"design":[6],"have":[7],"focused":[8],"on":[9,33,142],"immunogens":[10],"that":[11,199],"evoke":[12],"potent":[13],"neutralizing":[14,40,96,290],"antibody":[15,130,172,210],"responses":[16],"to":[17,49,128,166,194,260,272],"a":[18,68,79,156],"broad":[19],"spectrum":[20],"of":[21,28,38,82,94,160,208,223,245,252,284],"viruses":[22,84],"circulating":[23],"worldwide.":[24],"However,":[25],"the":[26,34,39,121,180,209,220,224,279],"development":[27],"effective":[29],"vaccines":[30],"will":[31],"depend":[32],"identification":[35,280],"and":[36,42,53,64,71,114,124,147,163,203,265,281],"characterization":[37],"antibodies":[41,98],"their":[43],"epitopes.":[44],"We":[45,116,154,187],"developed":[46],"bioinformatics":[47],"methods":[48,257],"predict":[50,129,266],"epitope":[51,131,173,214,238,267],"networks":[52,149,215,239,268],"antigenic":[54],"determinants":[55],"using":[56],"structural":[57],"information,":[58],"as":[59,61,137,170,197,237],"well":[60],"corresponding":[62],"genotypes":[63],"phenotypes":[65],"generated":[66],"by":[67,176,288],"highly":[69],"sensitive":[70],"reproducible":[72],"neutralization":[73,89,181,201,253],"assay.282":[74],"clonal":[75],"envelope":[76,122,152,225],"sequences":[77],"from":[78],"multiclade":[80],"panel":[81],"were":[85,135,216,258],"tested":[86],"viral":[88],"assays":[90],"with":[91,120,179,191,248,270],"an":[92],"array":[93],"broadly":[95,289],"monoclonal":[97,274],"(mAbs:":[99],"b12,":[100],"PG9,16,":[101],"PGT121":[102],"-":[103,106,109,112],"128,":[104],"PGT130":[105],"131,":[107],"PGT135":[108],"137,":[110],"PGT141":[111],"145,":[113],"PGV04).":[115],"correlated":[117],"IC50":[118,195],"titers":[119,196],"sequences,":[123],"used":[125],"this":[126],"information":[127],"networks.":[132],"Structural":[133],"patches":[134,169],"defined":[136],"amino":[138],"acid":[139],"groups":[140],"based":[141],"solvent-accessibility,":[143],"radius,":[144],"atomic":[145],"depth,":[146],"interaction":[148],"within":[150,219],"3D":[151],"models.":[153],"applied":[155],"boosted":[157],"algorithm":[158],"consisting":[159],"multiple":[161,241],"machine-learning":[162],"statistical":[164],"models":[165],"evaluate":[167],"these":[168,246],"possible":[171],"regions,":[174],"evidenced":[175],"strong":[177],"correlations":[178],"response":[182,271],"for":[183],"each":[184],"antibody.":[185],"RESULTS:":[186],"identified":[188,236],"patch":[189],"clusters":[190],"significant":[192],"correlation":[193],"sites":[198],"impact":[200],"sensitivity":[202],"therefore":[204],"are":[205],"potentially":[206],"part":[207],"binding":[211],"sites.":[212],"Predicted":[213],"mostly":[217],"located":[218],"variable":[221],"loops":[222],"glycoprotein":[226],"(gp120),":[227],"particularly":[228],"V1/V2.":[230],"Site-directed":[231],"mutagenesis":[232],"experiments":[233],"involving":[234],"residues":[235,247],"across":[240],"mAbs":[242],"confirmed":[243],"association":[244],"loss":[249],"or":[250],"gain":[251],"sensitivity.":[254],"CONCLUSIONS:":[255],"Computational":[256],"implemented":[259],"rapidly":[261],"survey":[262],"protein":[263],"structures":[264],"associated":[269],"individual":[273],"antibodies,":[275],"which":[276],"resulted":[277],"deeper":[282],"understanding":[283],"immunological":[285],"hotspots":[286],"targeted":[287],"antibodies.":[292]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
