{"id":"https://openalex.org/W2953176058","doi":"https://doi.org/10.1371/journal.pcbi.1006112","title":"RosettaAntibodyDesign (RAbD): A general framework for computational antibody design","display_name":"RosettaAntibodyDesign (RAbD): A general framework for computational antibody design","publication_year":2018,"publication_date":"2018-04-27","ids":{"openalex":"https://openalex.org/W2953176058","doi":"https://doi.org/10.1371/journal.pcbi.1006112","mag":"2953176058"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006112","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006112","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006112&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006112&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003957487","display_name":"Jared Adolf\u2010Bryfogle","orcid":"https://orcid.org/0000-0001-8586-1907"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]},{"id":"https://openalex.org/I1289437631","display_name":"Fox Chase Cancer Center","ror":"https://ror.org/0567t7073","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1289437631","https://openalex.org/I4210122924"]},{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jared Adolf-Bryfogle","raw_affiliation_strings":["Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, United States of America","Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA, United States of America","The Scripps Research Institute, La Jolla, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, United States of America","institution_ids":["https://openalex.org/I1289437631"]},{"raw_affiliation_string":"Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA, United States of America","institution_ids":["https://openalex.org/I72816309"]},{"raw_affiliation_string":"The Scripps Research Institute, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064936359","display_name":"Oleksandr Kalyuzhniy","orcid":"https://orcid.org/0000-0002-5273-1951"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]},{"id":"https://openalex.org/I1310987316","display_name":"International AIDS Vaccine Initiative","ror":"https://ror.org/05ayv2203","country_code":"US","type":"funder","lineage":["https://openalex.org/I1310987316"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Oleks Kalyuzhniy","raw_affiliation_strings":["IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, United States of America","The Scripps Research Institute, La Jolla, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I1310987316"]},{"raw_affiliation_string":"The Scripps Research Institute, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027498123","display_name":"Michael Kubitz","orcid":"https://orcid.org/0000-0002-3917-453X"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Kubitz","raw_affiliation_strings":["The Scripps Research Institute, La Jolla, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"The Scripps Research Institute, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068514328","display_name":"Brian D. Weitzner","orcid":"https://orcid.org/0000-0002-1909-0961"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian D. Weitzner","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, WA, United States of America","Institute for Protein Design, University of Washington, Seattle, WA, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, WA, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, WA, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006838546","display_name":"Xiaozhen Hu","orcid":"https://orcid.org/0000-0003-3890-0533"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaozhen Hu","raw_affiliation_strings":["The Scripps Research Institute, La Jolla, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"The Scripps Research Institute, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050272964","display_name":"Yumiko Adachi","orcid":"https://orcid.org/0000-0002-0795-9375"},"institutions":[{"id":"https://openalex.org/I1310987316","display_name":"International AIDS Vaccine Initiative","ror":"https://ror.org/05ayv2203","country_code":"US","type":"funder","lineage":["https://openalex.org/I1310987316"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yumiko Adachi","raw_affiliation_strings":["IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I1310987316"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067186373","display_name":"William R. Schief","orcid":"https://orcid.org/0000-0002-1120-0150"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]},{"id":"https://openalex.org/I1310987316","display_name":"International AIDS Vaccine Initiative","ror":"https://ror.org/05ayv2203","country_code":"US","type":"funder","lineage":["https://openalex.org/I1310987316"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William R. Schief","raw_affiliation_strings":["IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, United States of America","The Scripps Research Institute, La Jolla, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I1310987316"]},{"raw_affiliation_string":"The Scripps Research Institute, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053977807","display_name":"Roland L. Dunbrack","orcid":"https://orcid.org/0000-0001-7674-6667"},"institutions":[{"id":"https://openalex.org/I1289437631","display_name":"Fox Chase Cancer Center","ror":"https://ror.org/0567t7073","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1289437631","https://openalex.org/I4210122924"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Roland L. Dunbrack","raw_affiliation_strings":["Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, United States of America"],"affiliations":[{"raw_affiliation_string":"Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, United States of America","institution_ids":["https://openalex.org/I1289437631"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5053977807"],"corresponding_institution_ids":["https://openalex.org/I1289437631"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":10.9519,"has_fulltext":true,"cited_by_count":223,"citation_normalized_percentile":{"value":0.98859664,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"14","issue":"4","first_page":"e1006112","last_page":"e1006112"},"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9984999895095825,"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/T11124","display_name":"Protein purification and stability","score":0.9983999729156494,"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/computer-science","display_name":"Computer science","score":0.6377685070037842},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.5125401020050049},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5097529292106628},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.4705764651298523},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4668467938899994},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.45881280303001404},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3988950252532959},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.31122565269470215},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2242327332496643},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2073410451412201},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1903921663761139},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11153087019920349}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6377685070037842},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.5125401020050049},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5097529292106628},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.4705764651298523},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4668467938899994},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.45881280303001404},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3988950252532959},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.31122565269470215},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2242327332496643},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2073410451412201},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1903921663761139},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11153087019920349},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1006112","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006112","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006112&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1006112","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006112","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:25c7583215634d658b727758fbfe0bdf","is_oa":true,"landing_page_url":"https://doaj.org/article/25c7583215634d658b727758fbfe0bdf","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 14, Iss 4, p e1006112 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4875570","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5942852","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":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/6196769","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/RosettaAntibodyDesign_RAbD_A_general_framework_for_computational_antibody_design/6196769","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006112","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006112","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006112&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7599999904632568,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G1770244982","display_name":null,"funder_award_id":"P01 AI094419","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G2785242417","display_name":null,"funder_award_id":"R35 GM122517","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4253405033","display_name":null,"funder_award_id":"R01 GM111819","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2953176058.pdf","grobid_xml":"https://content.openalex.org/works/W2953176058.grobid-xml"},"referenced_works_count":138,"referenced_works":["https://openalex.org/W150416639","https://openalex.org/W1485730287","https://openalex.org/W1490966809","https://openalex.org/W1569245716","https://openalex.org/W1724277458","https://openalex.org/W1761553731","https://openalex.org/W1847500897","https://openalex.org/W1909149576","https://openalex.org/W1956208665","https://openalex.org/W1963480235","https://openalex.org/W1964126053","https://openalex.org/W1964421503","https://openalex.org/W1967351152","https://openalex.org/W1969407832","https://openalex.org/W1969644422","https://openalex.org/W1969761972","https://openalex.org/W1978398372","https://openalex.org/W1978499958","https://openalex.org/W1981848510","https://openalex.org/W1982679430","https://openalex.org/W1985445940","https://openalex.org/W1985743545","https://openalex.org/W1987696643","https://openalex.org/W1991235944","https://openalex.org/W1993575340","https://openalex.org/W1995044751","https://openalex.org/W1996581857","https://openalex.org/W1999648327","https://openalex.org/W2000443388","https://openalex.org/W2001842251","https://openalex.org/W2005169770","https://openalex.org/W2007746130","https://openalex.org/W2007804411","https://openalex.org/W2009008563","https://openalex.org/W2011261569","https://openalex.org/W2011658408","https://openalex.org/W2011690386","https://openalex.org/W2016240751","https://openalex.org/W2023423521","https://openalex.org/W2027918314","https://openalex.org/W2031132894","https://openalex.org/W2033969841","https://openalex.org/W2035942032","https://openalex.org/W2037956462","https://openalex.org/W2043162595","https://openalex.org/W2045266215","https://openalex.org/W2048313558","https://openalex.org/W2049275721","https://openalex.org/W2052332203","https://openalex.org/W2053134976","https://openalex.org/W2054357328","https://openalex.org/W2056034415","https://openalex.org/W2063062799","https://openalex.org/W2066244933","https://openalex.org/W2067484689","https://openalex.org/W2067608620","https://openalex.org/W2070360032","https://openalex.org/W2071704671","https://openalex.org/W2078070662","https://openalex.org/W2080057469","https://openalex.org/W2082260955","https://openalex.org/W2083028331","https://openalex.org/W2083982805","https://openalex.org/W2084493621","https://openalex.org/W2085414000","https://openalex.org/W2086108159","https://openalex.org/W2091751298","https://openalex.org/W2093607407","https://openalex.org/W2095837484","https://openalex.org/W2100717755","https://openalex.org/W2104455255","https://openalex.org/W2105273832","https://openalex.org/W2110270259","https://openalex.org/W2111387452","https://openalex.org/W2111410489","https://openalex.org/W2114559206","https://openalex.org/W2114747432","https://openalex.org/W2122851718","https://openalex.org/W2124106603","https://openalex.org/W2132793463","https://openalex.org/W2134758761","https://openalex.org/W2142840682","https://openalex.org/W2143210482","https://openalex.org/W2143467722","https://openalex.org/W2146134187","https://openalex.org/W2146522960","https://openalex.org/W2146773519","https://openalex.org/W2148895983","https://openalex.org/W2149662149","https://openalex.org/W2150633245","https://openalex.org/W2151581834","https://openalex.org/W2151721114","https://openalex.org/W2160415526","https://openalex.org/W2162210398","https://openalex.org/W2164130591","https://openalex.org/W2164958220","https://openalex.org/W2166103775","https://openalex.org/W2167404361","https://openalex.org/W2167795220","https://openalex.org/W2167833742","https://openalex.org/W2175294133","https://openalex.org/W2175687390","https://openalex.org/W2180048932","https://openalex.org/W2296574846","https://openalex.org/W2345741266","https://openalex.org/W2524536661","https://openalex.org/W2554770042","https://openalex.org/W2568203951","https://openalex.org/W2580666741","https://openalex.org/W2606439133","https://openalex.org/W2613081940","https://openalex.org/W2949117180","https://openalex.org/W3022984174","https://openalex.org/W3148398775","https://openalex.org/W4229880569","https://openalex.org/W4231357423","https://openalex.org/W4244300362","https://openalex.org/W4254419505","https://openalex.org/W4298064106","https://openalex.org/W4298440781","https://openalex.org/W6642737583","https://openalex.org/W6644899816","https://openalex.org/W6648910957","https://openalex.org/W6649647085","https://openalex.org/W6650382525","https://openalex.org/W6652520905","https://openalex.org/W6658906900","https://openalex.org/W6659446789","https://openalex.org/W6670905228","https://openalex.org/W6671573894","https://openalex.org/W6671957993","https://openalex.org/W6678410401","https://openalex.org/W6679831331","https://openalex.org/W6681507636","https://openalex.org/W6681661067","https://openalex.org/W6682562476","https://openalex.org/W6684507457","https://openalex.org/W6685269434"],"related_works":["https://openalex.org/W2132971779","https://openalex.org/W2152844235","https://openalex.org/W2376454312","https://openalex.org/W1988730649","https://openalex.org/W2095784700","https://openalex.org/W2170120749","https://openalex.org/W2067576503","https://openalex.org/W2199134476","https://openalex.org/W4372348062","https://openalex.org/W2170285690"],"abstract_inverted_index":{"A":[0],"structural-bioinformatics-based":[1],"computational":[2,168],"methodology":[3],"and":[4,25,54,92,133,154,187,236,256,268,285,326],"framework":[5],"have":[6],"been":[7],"developed":[8],"for":[9,38,164,229,262,283,287,299,305,334],"the":[10,21,39,65,179,191,199,210,216,230,244,249,259,266,271,296,300,309,312,321,324,332,340,343,350,357,369],"design":[11,40,82,99,149,172,202,211,291],"of":[12,16,28,41,47,64,68,89,129,142,181,183,193,195,233,246,248,270,323,337,361,368],"antibodies":[13,42],"to":[14,31,84,119,178,355],"targets":[15],"interest.":[17],"RosettaAntibodyDesign":[18],"(RAbD)":[19],"samples":[20,51,93],"diverse":[22,144],"sequence,":[23],"structure,":[24,114],"binding":[26],"space":[27],"an":[29,32,107,335],"antibody":[30,52],"antigen":[33,239,310,325],"in":[34,43,167,258,265,311,317,320,328],"highly":[35],"customizable":[36],"protocols":[37],"a":[44,60,97,121,140],"broad":[45],"range":[46],"applications.":[48],"The":[49,171,238],"program":[50],"sequences":[53],"structures":[55,58,314],"by":[56,190],"grafting":[57],"from":[59,106,222],"widely":[61],"accepted":[62],"set":[63,141],"canonical":[66],"clusters":[67,188,257],"CDRs":[69,126,232],"(North":[70],"et":[71],"al.,":[72],"J.":[73],"Mol.":[74],"Biol.,":[75],"406:228-256,":[76],"2011).":[77],"It":[78],"then":[79],"performs":[80],"sequence":[81,87,290,351],"according":[83],"amino":[85,251,302,358],"acid":[86,252,303,359],"profiles":[88,352],"each":[90],"cluster,":[91],"CDR":[94,103,123,185,254,294],"backbones":[95],"using":[96,147],"flexible-backbone":[98],"protocol":[100],"incorporating":[101],"cluster-based":[102],"constraints.":[104],"Starting":[105],"existing":[108],"experimental":[109],"or":[110,124],"computationally":[111],"modeled":[112],"antigen-antibody":[113],"RAbD":[115,138],"can":[116],"be":[117],"used":[118],"redesign":[120],"single":[122],"multiple":[125],"with":[127],"loops":[128],"different":[130],"length,":[131],"conformation,":[132],"sequence.":[134],"We":[135,159,226],"rigorously":[136],"benchmarked":[137],"on":[139],"60":[143],"antibody-antigen":[145],"complexes,":[146],"two":[148,161],"strategies-optimizing":[150],"total":[151],"Rosetta":[152],"energy":[153,157],"optimizing":[155],"interface":[156],"alone.":[158],"utilized":[160],"novel":[162],"metrics":[163],"measuring":[165],"success":[166],"protein":[169],"design.":[170],"risk":[173,240],"ratio":[174,241,245],"(DRR)":[175],"is":[176,213,243],"equal":[177],"frequency":[180,192],"recovery":[182,298,367],"native":[184,217,250,301,313],"lengths":[186],"divided":[189],"sampling":[194],"those":[196],"features":[197],"during":[198],"Monte":[200],"Carlo":[201],"procedure.":[203],"Ratios":[204],"greater":[205],"than":[206,220],"1.0":[207],"indicate":[208],"that":[209,307,349],"process":[212],"picking":[214],"out":[215],"more":[218],"frequently":[219],"expected":[221],"their":[223],"sampled":[224],"rate.":[225],"achieved":[227,276],"DRRs":[228],"non-H3":[231],"between":[234],"2.4":[235],"4.0.":[237],"(ARR)":[242],"frequencies":[247],"types,":[253],"lengths,":[255],"output":[260],"decoys":[261],"simulations":[263,292,318,329],"performed":[264,319,330],"presence":[267,322],"absence":[269],"antigen.":[272],"For":[273,289,339],"CDRs,":[274],"we":[275],"cluster":[277],"ARRs":[278],"as":[279,281],"high":[280],"2.5":[282],"L1":[284],"1.5":[286],"H2.":[288],"without":[293,331],"grafting,":[295],"overall":[297],"types":[304,360],"residues":[306],"contact":[308],"was":[315,345],"72%":[316],"48%":[327],"antigen,":[333],"ARR":[336,344],"1.5.":[338],"non-contacting":[341],"residues,":[342],"1.08.":[346],"This":[347],"shows":[348],"are":[353],"able":[354],"maintain":[356],"these":[362],"conserved,":[363],"buried":[364],"sites,":[365],"while":[366],"exposed,":[370],"contacting":[371]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":46},{"year":2024,"cited_by_count":47},{"year":2023,"cited_by_count":32},{"year":2022,"cited_by_count":27},{"year":2021,"cited_by_count":25},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":15},{"year":2018,"cited_by_count":5}],"updated_date":"2026-03-29T08:15:47.926485","created_date":"2025-10-10T00:00:00"}
