{"id":"https://openalex.org/W4401918526","doi":"https://doi.org/10.1021/acs.jcim.4c00711","title":"Antibody-SGM, a Score-Based Generative Model for Antibody Heavy-Chain Design","display_name":"Antibody-SGM, a Score-Based Generative Model for Antibody Heavy-Chain Design","publication_year":2024,"publication_date":"2024-08-27","ids":{"openalex":"https://openalex.org/W4401918526","doi":"https://doi.org/10.1021/acs.jcim.4c00711","pmid":"https://pubmed.ncbi.nlm.nih.gov/39189360"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c00711","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00711","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085261504","display_name":"Xuezhi Xie","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Xuezhi Xie","raw_affiliation_strings":["Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada","Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047852894","display_name":"Pedro A. Valiente","orcid":"https://orcid.org/0000-0002-4776-6017"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Pedro A. Valiente","raw_affiliation_strings":["Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"affiliations":[{"raw_affiliation_string":"Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038183595","display_name":"Jin Sub Lee","orcid":"https://orcid.org/0000-0002-6410-2706"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jin Sub Lee","raw_affiliation_strings":["Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada","Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100320583","display_name":"Ji\u2010Sun Kim","orcid":"https://orcid.org/0000-0002-9568-1114"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jisun Kim","raw_affiliation_strings":["Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"affiliations":[{"raw_affiliation_string":"Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043262709","display_name":"Philip M. Kim","orcid":"https://orcid.org/0000-0003-3683-152X"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Philip M. Kim","raw_affiliation_strings":["Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada","Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada","Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5043262709"],"corresponding_institution_ids":["https://openalex.org/I185261750"],"apc_list":null,"apc_paid":null,"fwci":1.5678,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.83444681,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"64","issue":"17","first_page":"6745","last_page":"6757"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11124","display_name":"Protein purification and stability","score":0.9983000159263611,"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":0.9968000054359436,"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":0.6565537452697754},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4742671251296997},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46928083896636963},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.4571400284767151},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.43459463119506836},{"id":"https://openalex.org/keywords/protein-engineering","display_name":"Protein engineering","score":0.4151086211204529},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.31517893075942993},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.2696378529071808},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.25172945857048035},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18185940384864807},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1058761477470398}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6565537452697754},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4742671251296997},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46928083896636963},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.4571400284767151},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.43459463119506836},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.4151086211204529},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31517893075942993},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2696378529071808},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.25172945857048035},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18185940384864807},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1058761477470398},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007143","descriptor_name":"Immunoglobulin Heavy Chains","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D007143","descriptor_name":"Immunoglobulin Heavy Chains","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D007143","descriptor_name":"Immunoglobulin Heavy Chains","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D007143","descriptor_name":"Immunoglobulin Heavy Chains","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D007143","descriptor_name":"Immunoglobulin Heavy Chains","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D007143","descriptor_name":"Immunoglobulin Heavy Chains","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.4c00711","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00711","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:39189360","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39189360","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1806205260","display_name":null,"funder_award_id":"PJT-153279","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G1949702599","display_name":null,"funder_award_id":"PJT-166008","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"}],"funders":[{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1976499671","https://openalex.org/W1978499958","https://openalex.org/W1982679430","https://openalex.org/W2005140643","https://openalex.org/W2035991134","https://openalex.org/W2110505462","https://openalex.org/W2163418557","https://openalex.org/W2206954826","https://openalex.org/W2263209021","https://openalex.org/W2555870966","https://openalex.org/W2563705555","https://openalex.org/W2583289470","https://openalex.org/W2980789587","https://openalex.org/W2990138404","https://openalex.org/W2997234557","https://openalex.org/W3042825269","https://openalex.org/W3135044423","https://openalex.org/W3154275519","https://openalex.org/W3212854871","https://openalex.org/W4205953903","https://openalex.org/W4210520848","https://openalex.org/W4281619315","https://openalex.org/W4283588088","https://openalex.org/W4285010209","https://openalex.org/W4317212859","https://openalex.org/W4368374143","https://openalex.org/W4376108605","https://openalex.org/W4378714914","https://openalex.org/W4383957026","https://openalex.org/W4393971152","https://openalex.org/W4396721167"],"related_works":["https://openalex.org/W2116266427","https://openalex.org/W2991041010","https://openalex.org/W2003675367","https://openalex.org/W2991203454","https://openalex.org/W2512252615","https://openalex.org/W2409023191","https://openalex.org/W3215076145","https://openalex.org/W2005982196","https://openalex.org/W1534529517","https://openalex.org/W4390745893"],"abstract_inverted_index":{"Traditional":[0],"computational":[1],"methods":[2,35],"for":[3,14,29,183],"antibody":[4,102,143,155],"design":[5,136,193],"involved":[6],"random":[7,119],"mutagenesis":[8],"followed":[9],"by":[10,105],"energy":[11],"function":[12,164],"assessment":[13],"candidate":[15],"selection.":[16],"Recently,":[17],"diffusion":[18,70],"models":[19],"have":[20],"garnered":[21],"considerable":[22],"attention":[23],"as":[24],"cutting-edge":[25],"generative":[26],"models,":[27,84],"lauded":[28],"their":[30],"remarkable":[31],"performance.":[32],"However,":[33],"these":[34],"often":[36],"focus":[37],"solely":[38],"on":[39],"the":[40,46,50,59,74,94,107,135,151,178,189],"backbone":[41,79],"or":[42],"sequence,":[43],"resulting":[44],"in":[45],"incomplete":[47],"depiction":[48],"of":[49,76,113,126,137,153,180,191],"overall":[51],"structure":[52,173],"and":[53,90,115,121,150,157,172,186],"necessitating":[54],"additional":[55],"techniques":[56],"to":[57,109],"predict":[58],"missing":[60],"component.":[61],"This":[62],"study":[63],"presents":[64],"Antibody-SGM,":[65],"an":[66],"innovative":[67],"joint":[68],"structure-sequence":[69],"model":[71],"that":[72],"addresses":[73],"limitations":[75],"existing":[77],"protein":[78,163,184,192],"generation":[80,95,108],"models.":[81,194],"Unlike":[82],"previous":[83],"Antibody-SGM":[85,160],"successfully":[86],"integrates":[87],"sequence-specific":[88],"attributes":[89],"functional":[91],"properties":[92],"into":[93],"process.":[96],"Our":[97],"methodology":[98],"generates":[99],"full-atom":[100,138],"native-like":[101],"heavy":[103,144],"chains":[104,145],"refining":[106],"create":[110],"valid":[111],"pairs":[112],"sequences":[114,120,156],"structures,":[116],"starting":[117],"with":[118,148],"structural":[122,158],"properties.":[123],"The":[124],"versatility":[125],"our":[127,181],"method":[128],"is":[129],"demonstrated":[130],"through":[131,165],"various":[132],"applications,":[133],"including":[134],"antibodies,":[139],"antigen-specific":[140],"CDR":[141],"design,":[142],"optimization,":[146],"validation":[147],"Alphafold3,":[149],"identification":[152],"crucial":[154],"features.":[159],"also":[161],"optimizes":[162],"active":[166],"inpainting":[167],"learning,":[168],"allowing":[169],"simultaneous":[170],"sequence":[171],"optimization.":[174],"These":[175],"improvements":[176],"demonstrate":[177],"promise":[179],"strategy":[182],"engineering":[185],"significantly":[187],"increase":[188],"power":[190]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2026-04-15T08:11:43.952461","created_date":"2025-10-10T00:00:00"}
