{"id":"https://openalex.org/W2110298304","doi":"https://doi.org/10.1186/1471-2105-9-514","title":"ElliPro: a new structure-based tool for the prediction of antibody epitopes","display_name":"ElliPro: a new structure-based tool for the prediction of antibody epitopes","publication_year":2008,"publication_date":"2008-12-01","ids":{"openalex":"https://openalex.org/W2110298304","doi":"https://doi.org/10.1186/1471-2105-9-514","mag":"2110298304","pmid":"https://pubmed.ncbi.nlm.nih.gov/19055730"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-514","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-514","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-514","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/10.1186/1471-2105-9-514","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070141127","display_name":"Julia Ponomarenko","orcid":"https://orcid.org/0000-0002-1477-9444"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I6750721","display_name":"University of Montana","ror":"https://ror.org/0078xmk34","country_code":"US","type":"education","lineage":["https://openalex.org/I6750721"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julia Ponomarenko","raw_affiliation_strings":["San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. jpon@sdsc.edu","Skaggs School of Pharmacy and Pharmaceutical Sciences,University of California,San Diego, La Jolla, USA","San Diego Supercomputer Center, University of California San Diego, La Jolla, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. jpon@sdsc.edu","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences,University of California,San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I6750721"]},{"raw_affiliation_string":"San Diego Supercomputer Center, University of California San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076329672","display_name":"Huynh\u2010Hoa Bui","orcid":null},"institutions":[{"id":"https://openalex.org/I2800035258","display_name":"Ionis Pharmaceuticals (United States)","ror":"https://ror.org/00t8bew53","country_code":"US","type":"company","lineage":["https://openalex.org/I2800035258"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Huynh-Hoa Bui","raw_affiliation_strings":["Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad, California, 92008, USA","Isis Pharmaceuticals, Inc, Carlsbad, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad, California, 92008, USA","institution_ids":["https://openalex.org/I2800035258"]},{"raw_affiliation_string":"Isis Pharmaceuticals, Inc, Carlsbad, USA","institution_ids":["https://openalex.org/I2800035258"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103739540","display_name":"Wei Li","orcid":"https://orcid.org/0000-0003-3389-6977"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I6750721","display_name":"University of Montana","ror":"https://ror.org/0078xmk34","country_code":"US","type":"education","lineage":["https://openalex.org/I6750721"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Li","raw_affiliation_strings":["Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA","institution_ids":["https://openalex.org/I6750721","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066652370","display_name":"Nicholas Fusseder","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nicholas Fusseder","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075833022","display_name":"Philip E. Bourne","orcid":"https://orcid.org/0000-0002-7618-7292"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I6750721","display_name":"University of Montana","ror":"https://ror.org/0078xmk34","country_code":"US","type":"education","lineage":["https://openalex.org/I6750721"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philip E Bourne","raw_affiliation_strings":["San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA","Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA","Skaggs School of Pharmacy and Pharmaceutical Sciences,University of California,San Diego, La Jolla, USA","San Diego Supercomputer Center, University of California San Diego, La Jolla, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA","institution_ids":["https://openalex.org/I6750721","https://openalex.org/I36258959"]},{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences,University of California,San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I6750721"]},{"raw_affiliation_string":"San Diego Supercomputer Center, University of California San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010966529","display_name":"Alessandro Sette","orcid":"https://orcid.org/0000-0001-7013-2250"},"institutions":[{"id":"https://openalex.org/I1311191458","display_name":"La Jolla Institute for Immunology","ror":"https://ror.org/05vkpd318","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1311191458"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alessandro Sette","raw_affiliation_strings":["La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037, USA","La Jolla Institute for Allergy & Immunology, La Jolla, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037, USA","institution_ids":["https://openalex.org/I1311191458"]},{"raw_affiliation_string":"La Jolla Institute for Allergy & Immunology, La Jolla, USA","institution_ids":["https://openalex.org/I1311191458"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023547268","display_name":"Bjoern Peters","orcid":"https://orcid.org/0000-0002-8457-6693"},"institutions":[{"id":"https://openalex.org/I1311191458","display_name":"La Jolla Institute for Immunology","ror":"https://ror.org/05vkpd318","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1311191458"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bjoern Peters","raw_affiliation_strings":["La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037, USA","La Jolla Institute for Allergy & Immunology, La Jolla, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037, USA","institution_ids":["https://openalex.org/I1311191458"]},{"raw_affiliation_string":"La Jolla Institute for Allergy & Immunology, La Jolla, USA","institution_ids":["https://openalex.org/I1311191458"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":5.4757,"has_fulltext":true,"cited_by_count":1721,"citation_normalized_percentile":{"value":0.96590468,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"9","issue":"1","first_page":"514","last_page":"514"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9873999953269958,"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":0.9873999953269958,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.005499999970197678,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.0015999999595806003,"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":0.9634420871734619},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6407434344291687},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5552435517311096},{"id":"https://openalex.org/keywords/linear-epitope","display_name":"Linear epitope","score":0.5400550961494446},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.5101625919342041},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.4320133328437805},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40600407123565674},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18489453196525574},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10916298627853394}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.9634420871734619},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6407434344291687},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5552435517311096},{"id":"https://openalex.org/C78598654","wikidata":"https://www.wikidata.org/wiki/Q17140316","display_name":"Linear epitope","level":4,"score":0.5400550961494446},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.5101625919342041},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.4320133328437805},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40600407123565674},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18489453196525574},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10916298627853394}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"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":"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018448","descriptor_name":"Models, Immunological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018448","descriptor_name":"Models, Immunological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018448","descriptor_name":"Models, Immunological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018604","descriptor_name":"Epitope Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018604","descriptor_name":"Epitope Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018604","descriptor_name":"Epitope Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-9-514","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-514","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-514","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:19055730","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19055730","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:ark:/13030/qt9wm6009w","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:839f1752f70d4f55ac801d42f0e4267c","is_oa":false,"landing_page_url":"https://doaj.org/article/839f1752f70d4f55ac801d42f0e4267c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss 1, p 514 (2008)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt9wm6009w","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/9wm6009w","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC bioinformatics, vol 9, iss 1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2607291","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2607291","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:10.1186/1471-2105-9-514","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-514","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-514","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":[{"display_name":"Reduced inequalities","score":0.550000011920929,"id":"https://metadata.un.org/sdg/10"},{"display_name":"Peace, Justice and strong institutions","score":0.4699999988079071,"id":"https://metadata.un.org/sdg/16"}],"awards":[{"id":"https://openalex.org/G116422006","display_name":null,"funder_award_id":"HHSN26620040006C","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2110298304.pdf","grobid_xml":"https://content.openalex.org/works/W2110298304.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1607931568","https://openalex.org/W1844925375","https://openalex.org/W2005707709","https://openalex.org/W2006386471","https://openalex.org/W2042492527","https://openalex.org/W2043699100","https://openalex.org/W2048848017","https://openalex.org/W2055043387","https://openalex.org/W2061365506","https://openalex.org/W2067570700","https://openalex.org/W2091852797","https://openalex.org/W2113530505","https://openalex.org/W2130479394","https://openalex.org/W2133872562","https://openalex.org/W2137575262","https://openalex.org/W2140468230","https://openalex.org/W2148219066","https://openalex.org/W2149984099","https://openalex.org/W2158698691","https://openalex.org/W2158781610","https://openalex.org/W2163462520","https://openalex.org/W2399825601","https://openalex.org/W2519703809"],"related_works":["https://openalex.org/W3145510187","https://openalex.org/W2003116223","https://openalex.org/W3096915742","https://openalex.org/W1991572753","https://openalex.org/W3139969521","https://openalex.org/W4241031629","https://openalex.org/W1996102030","https://openalex.org/W2062700146","https://openalex.org/W2029383042","https://openalex.org/W2205639271"],"abstract_inverted_index":{"BACKGROUND:":[0],"Reliable":[1],"prediction":[2,107,167,179],"of":[3,16,55,77,110,128,135,161,176,191,248,266],"antibody,":[4],"or":[5,118],"B-cell,":[6],"epitopes":[7,42,72,112,130,207,227,233],"remains":[8],"challenging":[9],"yet":[10],"highly":[11],"desirable":[12],"for":[13,39,149,170,187,204,262],"the":[14,44,49,75,98,102,106,154,164,174,177,184,245],"design":[15],"vaccines":[17],"and":[18,26,34,66,101,108,156,193,251],"immunodiagnostics.":[19],"A":[20],"correlation":[21],"between":[22],"antigenicity,":[23],"solvent":[24],"accessibility,":[25],"flexibility":[27],"in":[28,43,113,183,208],"proteins":[29,192],"was":[30,58,168,180],"demonstrated.":[31],"Subsequently,":[32],"Thornton":[33],"colleagues":[35],"proposed":[36],"a":[37,64,85,94,114,125,200],"method":[38,62,90],"identifying":[40,205],"continuous":[41],"protein":[45,116,209,249],"regions":[46],"protruding":[47],"from":[48,74,132,219,234],"protein's":[50],"globular":[51],"surface.":[52],"The":[53,217],"aim":[54],"this":[56],"work":[57],"to":[59],"implement":[60],"that":[61,87,145,222,231],"as":[63],"web-tool":[65,86],"evaluate":[67],"its":[68],"performance":[69],"on":[70,124,225,244],"discontinuous":[71,129],"known":[73],"structures":[76,134],"antibody-protein":[78,136],"complexes.":[79,137],"RESULTS:":[80],"Here":[81],"we":[82],"present":[83],"ElliPro,":[84],"implements":[88],"Thornton's":[89],"and,":[91],"together":[92],"with":[93,140],"residue":[95],"clustering":[96],"algorithm,":[97],"MODELLER":[99],"program":[100],"Jmol":[103],"viewer,":[104],"allows":[105],"visualization":[109],"antibody":[111,206,226],"given":[115],"sequence":[117],"structure.":[119],"ElliPro":[120,152,197,211,220,241],"has":[121],"been":[122],"tested":[123],"benchmark":[126],"dataset":[127],"inferred":[131],"3D":[133],"In":[138],"comparison":[139],"six":[141],"other":[142],"structure-based":[143],"methods":[144],"can":[146],"be":[147,258],"used":[148],"epitope":[150],"prediction,":[151],"performed":[153],"best":[155,178],"gave":[157],"an":[158],"AUC":[159],"value":[160],"0.732,":[162],"when":[163],"most":[165,182],"significant":[166],"considered":[169,199],"each":[171],"protein.":[172],"Since":[173],"rank":[175],"at":[181,214],"top":[185],"three":[186],"more":[188,229,259],"than":[189],"70%":[190],"never":[194],"exceeded":[195],"five,":[196],"is":[198,212,242],"useful":[201],"research":[202,224],"tool":[203],"antigens.":[210],"available":[213],"http://tools.immuneepitope.org/tools/ElliPro.":[215],"CONCLUSION:":[216],"results":[218],"suggest":[221],"further":[223,237],"considering":[228],"features":[230],"discriminate":[232],"non-epitopes":[235],"may":[236],"improve":[238],"predictions.":[239],"As":[240],"based":[243],"geometrical":[246],"properties":[247],"structure":[250],"does":[252],"not":[253],"require":[254],"training,":[255],"it":[256],"might":[257],"generally":[260],"applied":[261],"predicting":[263],"different":[264],"types":[265],"protein-protein":[267],"interactions.":[268]},"counts_by_year":[{"year":2026,"cited_by_count":86},{"year":2025,"cited_by_count":258},{"year":2024,"cited_by_count":229},{"year":2023,"cited_by_count":205},{"year":2022,"cited_by_count":204},{"year":2021,"cited_by_count":188},{"year":2020,"cited_by_count":197},{"year":2019,"cited_by_count":67},{"year":2018,"cited_by_count":54},{"year":2017,"cited_by_count":44},{"year":2016,"cited_by_count":35},{"year":2015,"cited_by_count":39},{"year":2014,"cited_by_count":23},{"year":2013,"cited_by_count":27},{"year":2012,"cited_by_count":25}],"updated_date":"2026-06-13T07:54:00.901334","created_date":"2025-10-10T00:00:00"}
