{"id":"https://openalex.org/W4408884143","doi":"https://doi.org/10.1093/bioinformatics/btaf129","title":"AI-augmented physics-based docking for antibody-antigen complex prediction","display_name":"AI-augmented physics-based docking for antibody-antigen complex prediction","publication_year":2025,"publication_date":"2025-03-23","ids":{"openalex":"https://openalex.org/W4408884143","doi":"https://doi.org/10.1093/bioinformatics/btaf129","pmid":"https://pubmed.ncbi.nlm.nih.gov/40135432"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf129","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf129","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf129/62728359/btaf129.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf129/62728359/btaf129.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102759372","display_name":"Francis Gaudreault","orcid":"https://orcid.org/0000-0001-5656-3118"},"institutions":[{"id":"https://openalex.org/I4210159778","display_name":"National Research Council Canada","ror":"https://ror.org/04mte1k06","country_code":"CA","type":"government","lineage":["https://openalex.org/I4210159778"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Francis Gaudreault","raw_affiliation_strings":["Human Health Therapeutics Research Centre, National Research Council Canada , Montreal, Quebec H4P 2R2,","National Research Council Canada Human Health Therapeutics Research Centre, , Montreal, Quebec H4P 2R2,"],"affiliations":[{"raw_affiliation_string":"Human Health Therapeutics Research Centre, National Research Council Canada , Montreal, Quebec H4P 2R2,","institution_ids":["https://openalex.org/I4210159778"]},{"raw_affiliation_string":"National Research Council Canada Human Health Therapeutics Research Centre, , Montreal, Quebec H4P 2R2,","institution_ids":["https://openalex.org/I4210159778"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019972390","display_name":"Traian Sulea","orcid":"https://orcid.org/0000-0001-5301-8261"},"institutions":[{"id":"https://openalex.org/I4210140149","display_name":"Ste. Anne's Hospital","ror":"https://ror.org/04b64cp31","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I4210140149"]},{"id":"https://openalex.org/I4210159778","display_name":"National Research Council Canada","ror":"https://ror.org/04mte1k06","country_code":"CA","type":"government","lineage":["https://openalex.org/I4210159778"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Traian Sulea","raw_affiliation_strings":["Human Health Therapeutics Research Centre, National Research Council Canada , Montreal, Quebec H4P 2R2,","Institute of Parasitology, McGill University , Sainte-Anne-de-Bellevue, Quebec H9X 3V9,","McGill University Institute of Parasitology, , Sainte\u2011Anne\u2011de\u2011Bellevue, Quebec H9X 3V9,","National Research Council Canada Human Health Therapeutics Research Centre, , Montreal, Quebec H4P 2R2,"],"affiliations":[{"raw_affiliation_string":"Human Health Therapeutics Research Centre, National Research Council Canada , Montreal, Quebec H4P 2R2,","institution_ids":["https://openalex.org/I4210159778"]},{"raw_affiliation_string":"Institute of Parasitology, McGill University , Sainte-Anne-de-Bellevue, Quebec H9X 3V9,","institution_ids":["https://openalex.org/I5023651","https://openalex.org/I4210140149"]},{"raw_affiliation_string":"McGill University Institute of Parasitology, , Sainte\u2011Anne\u2011de\u2011Bellevue, Quebec H9X 3V9,","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"National Research Council Canada Human Health Therapeutics Research Centre, , Montreal, Quebec H4P 2R2,","institution_ids":["https://openalex.org/I4210159778"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005015476","display_name":"Christopher R. Corbeil","orcid":"https://orcid.org/0000-0001-7657-0286"},"institutions":[{"id":"https://openalex.org/I4210159778","display_name":"National Research Council Canada","ror":"https://ror.org/04mte1k06","country_code":"CA","type":"government","lineage":["https://openalex.org/I4210159778"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Christopher R Corbeil","raw_affiliation_strings":["Department of Biochemistry, McGill University , Montreal, Quebec H3A 1A3,","Human Health Therapeutics Research Centre, National Research Council Canada , Montreal, Quebec H4P 2R2,","National Research Council Canada Human Health Therapeutics Research Centre, , Montreal, Quebec H4P 2R2,","McGill University Department of Biochemistry, , Montreal, Quebec H3A 1A3,"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, McGill University , Montreal, Quebec H3A 1A3,","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Human Health Therapeutics Research Centre, National Research Council Canada , Montreal, Quebec H4P 2R2,","institution_ids":["https://openalex.org/I4210159778"]},{"raw_affiliation_string":"National Research Council Canada Human Health Therapeutics Research Centre, , Montreal, Quebec H4P 2R2,","institution_ids":["https://openalex.org/I4210159778"]},{"raw_affiliation_string":"McGill University Department of Biochemistry, , Montreal, Quebec H3A 1A3,","institution_ids":["https://openalex.org/I5023651"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5102759372"],"corresponding_institution_ids":["https://openalex.org/I4210159778"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":8.2572,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.97515226,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"41","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9998999834060669,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.995199978351593,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9926000237464905,"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/docking","display_name":"Docking (animal)","score":0.8268929719924927},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.594255805015564},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43417614698410034},{"id":"https://openalex.org/keywords/macromolecular-docking","display_name":"Macromolecular docking","score":0.43191877007484436},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.4132433533668518},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4096395671367645},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.28618133068084717},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20628267526626587},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.1859743297100067}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8268929719924927},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.594255805015564},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43417614698410034},{"id":"https://openalex.org/C116887118","wikidata":"https://www.wikidata.org/wiki/Q836685","display_name":"Macromolecular docking","level":3,"score":0.43191877007484436},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.4132433533668518},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4096395671367645},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.28618133068084717},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20628267526626587},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.1859743297100067},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000936","descriptor_name":"Antigen-Antibody Complex","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000936","descriptor_name":"Antigen-Antibody Complex","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000936","descriptor_name":"Antigen-Antibody Complex","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018604","descriptor_name":"Epitope Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018604","descriptor_name":"Epitope Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018604","descriptor_name":"Epitope Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf129","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf129","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf129/62728359/btaf129.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40135432","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40135432","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11978387","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11978387","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf129","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf129","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf129/62728359/btaf129.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4408884143.pdf"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1979284950","https://openalex.org/W2037312364","https://openalex.org/W2044551208","https://openalex.org/W2045266215","https://openalex.org/W2058017150","https://openalex.org/W2067608620","https://openalex.org/W2074719974","https://openalex.org/W2074726906","https://openalex.org/W2081941519","https://openalex.org/W2083734879","https://openalex.org/W2106648157","https://openalex.org/W2110062635","https://openalex.org/W2110505462","https://openalex.org/W2122199548","https://openalex.org/W2129454543","https://openalex.org/W2133712572","https://openalex.org/W2151581834","https://openalex.org/W2153983456","https://openalex.org/W2205853722","https://openalex.org/W2508425869","https://openalex.org/W2740434728","https://openalex.org/W2887788718","https://openalex.org/W2909020241","https://openalex.org/W2947363422","https://openalex.org/W3004009671","https://openalex.org/W3048109295","https://openalex.org/W3177828909","https://openalex.org/W4281790889","https://openalex.org/W4285392187","https://openalex.org/W4310159409","https://openalex.org/W4366823175","https://openalex.org/W4366998330","https://openalex.org/W4378714914","https://openalex.org/W4386121941","https://openalex.org/W4386713035","https://openalex.org/W4386793933","https://openalex.org/W4388020856","https://openalex.org/W4388627063","https://openalex.org/W4388870365","https://openalex.org/W4392761710","https://openalex.org/W4396721167"],"related_works":["https://openalex.org/W2585040066","https://openalex.org/W2996908194","https://openalex.org/W2205639271","https://openalex.org/W2162380182","https://openalex.org/W3005126098","https://openalex.org/W2157273785","https://openalex.org/W2862730334","https://openalex.org/W3011103292","https://openalex.org/W1489925612","https://openalex.org/W4400485740"],"abstract_inverted_index":{"The":[0],"AF2":[1],"rescoring":[2],"scripts":[3],"are":[4],"available":[5],"at":[6],"github.com/gaudreaultfnrc/AF2-Rescoring.":[7]},"counts_by_year":[{"year":2025,"cited_by_count":6}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
