{"id":"https://openalex.org/W4417267344","doi":"https://doi.org/10.1093/bib/bbaf658","title":"HuAbDiffusion: a discrete language diffusion model used for antibody humanization","display_name":"HuAbDiffusion: a discrete language diffusion model used for antibody humanization","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W4417267344","doi":"https://doi.org/10.1093/bib/bbaf658","pmid":"https://pubmed.ncbi.nlm.nih.gov/41370632"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf658","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf658","pdf_url":"https://academic.oup.com/bib/article-pdf/26/6/bbaf658/65831483/bbaf658.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/26/6/bbaf658/65831483/bbaf658.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Dongping Liu","orcid":"https://orcid.org/0009-0004-2101-3289"},"institutions":[{"id":"https://openalex.org/I4210118639","display_name":"Evive Biotech (China)","ror":"https://ror.org/02f6hqb19","country_code":"CN","type":"company","lineage":["https://openalex.org/I4210118639"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongping Liu","raw_affiliation_strings":["Production and R&D Center I of LSS (Life Science Service), GenScript Biotech Corporation , No. 28, Yongxi Rd, Nanjing, Jiangsu 211100 ,"],"raw_orcid":"https://orcid.org/0009-0004-2101-3289","affiliations":[{"raw_affiliation_string":"Production and R&D Center I of LSS (Life Science Service), GenScript Biotech Corporation , No. 28, Yongxi Rd, Nanjing, Jiangsu 211100 ,","institution_ids":["https://openalex.org/I4210118639"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113902481","display_name":"Xiaohu Hao","orcid":null},"institutions":[{"id":"https://openalex.org/I4210118639","display_name":"Evive Biotech (China)","ror":"https://ror.org/02f6hqb19","country_code":"CN","type":"company","lineage":["https://openalex.org/I4210118639"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaohu Hao","raw_affiliation_strings":["Production and R&D Center I of LSS (Life Science Service), GenScript Biotech Corporation , No. 28, Yongxi Rd, Nanjing, Jiangsu 211100 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Production and R&D Center I of LSS (Life Science Service), GenScript Biotech Corporation , No. 28, Yongxi Rd, Nanjing, Jiangsu 211100 ,","institution_ids":["https://openalex.org/I4210118639"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060417628","display_name":"Long Fan","orcid":"https://orcid.org/0000-0001-8938-2225"},"institutions":[{"id":"https://openalex.org/I4210118639","display_name":"Evive Biotech (China)","ror":"https://ror.org/02f6hqb19","country_code":"CN","type":"company","lineage":["https://openalex.org/I4210118639"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Long Fan","raw_affiliation_strings":["Production and R&D Center I of LSS (Life Science Service), GenScript (Shanghai) Biotech Corporation , No. 186, Hedan Rd, Shanghai Municipality 200100 ,","Production and R&D Center I of LSS (Life Science Service), GenScript Biotech Corporation , No. 28, Yongxi Rd, Nanjing, Jiangsu 211100 ,"],"raw_orcid":"https://orcid.org/0000-0001-8938-2225","affiliations":[{"raw_affiliation_string":"Production and R&D Center I of LSS (Life Science Service), GenScript (Shanghai) Biotech Corporation , No. 186, Hedan Rd, Shanghai Municipality 200100 ,","institution_ids":["https://openalex.org/I4210118639"]},{"raw_affiliation_string":"Production and R&D Center I of LSS (Life Science Service), GenScript Biotech Corporation , No. 28, Yongxi Rd, Nanjing, Jiangsu 211100 ,","institution_ids":["https://openalex.org/I4210118639"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.0182,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.82591818,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"26","issue":"6","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":0.9627000093460083,"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":0.9627000093460083,"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":0.020800000056624413,"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":0.005100000184029341,"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/antibody","display_name":"Antibody","score":0.7128000259399414},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.5414999723434448},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.4262999892234802},{"id":"https://openalex.org/keywords/basis","display_name":"Basis (linear algebra)","score":0.4147999882698059},{"id":"https://openalex.org/keywords/humanized-mouse","display_name":"Humanized mouse","score":0.38089999556541443},{"id":"https://openalex.org/keywords/humanized-antibody","display_name":"Humanized antibody","score":0.36239999532699585}],"concepts":[{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.7128000259399414},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5827999711036682},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.5414999723434448},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.4262999892234802},{"id":"https://openalex.org/C12426560","wikidata":"https://www.wikidata.org/wiki/Q189569","display_name":"Basis (linear algebra)","level":2,"score":0.4147999882698059},{"id":"https://openalex.org/C2776156784","wikidata":"https://www.wikidata.org/wiki/Q3491954","display_name":"Humanized mouse","level":3,"score":0.38089999556541443},{"id":"https://openalex.org/C2777092746","wikidata":"https://www.wikidata.org/wiki/Q5939625","display_name":"Humanized antibody","level":4,"score":0.36239999532699585},{"id":"https://openalex.org/C3020495827","wikidata":"https://www.wikidata.org/wiki/Q426141","display_name":"Bispecific antibody","level":4,"score":0.34470000863075256},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34040001034736633},{"id":"https://openalex.org/C542903549","wikidata":"https://www.wikidata.org/wiki/Q422248","display_name":"Monoclonal antibody","level":3,"score":0.33629998564720154},{"id":"https://openalex.org/C55689738","wikidata":"https://www.wikidata.org/wiki/Q15963867","display_name":"Discrete time and continuous time","level":2,"score":0.33079999685287476},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.287200003862381},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.28679999709129333},{"id":"https://openalex.org/C2777267654","wikidata":"https://www.wikidata.org/wiki/Q3519023","display_name":"Test (biology)","level":2,"score":0.267300009727478},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.25940001010894775}],"mesh":[{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","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":"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":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D061067","descriptor_name":"Antibodies, Monoclonal, Humanized","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf658","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf658","pdf_url":"https://academic.oup.com/bib/article-pdf/26/6/bbaf658/65831483/bbaf658.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41370632","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41370632","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12694429","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12694429/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12694429/pdf/bbaf658.pdf","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf658","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf658","pdf_url":"https://academic.oup.com/bib/article-pdf/26/6/bbaf658/65831483/bbaf658.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321605","display_name":"Government of Jiangsu Province","ror":"https://ror.org/004svx814"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4417267344.pdf","grobid_xml":"https://content.openalex.org/works/W4417267344.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1855237549","https://openalex.org/W1978499958","https://openalex.org/W1983494459","https://openalex.org/W1989451953","https://openalex.org/W1998383538","https://openalex.org/W2004714495","https://openalex.org/W2009573319","https://openalex.org/W2028450449","https://openalex.org/W2037914743","https://openalex.org/W2041741213","https://openalex.org/W2075097399","https://openalex.org/W2078070662","https://openalex.org/W2098154603","https://openalex.org/W2105521580","https://openalex.org/W2117246959","https://openalex.org/W2123708888","https://openalex.org/W2140674483","https://openalex.org/W2142678478","https://openalex.org/W2161151688","https://openalex.org/W2578029714","https://openalex.org/W2893755931","https://openalex.org/W2974982237","https://openalex.org/W2999958881","https://openalex.org/W3036167779","https://openalex.org/W3146944767","https://openalex.org/W3169434891","https://openalex.org/W3177828909","https://openalex.org/W3206187363","https://openalex.org/W4220757565","https://openalex.org/W4237589493","https://openalex.org/W4281690218","https://openalex.org/W4286561182","https://openalex.org/W4287083626","https://openalex.org/W4296032638","https://openalex.org/W4310420099","https://openalex.org/W4319842310","https://openalex.org/W4366520892","https://openalex.org/W4366823175","https://openalex.org/W4383957026","https://openalex.org/W4386629205","https://openalex.org/W4390880595","https://openalex.org/W4392270874","https://openalex.org/W4392576359","https://openalex.org/W4399258661","https://openalex.org/W4403324307","https://openalex.org/W4403329018","https://openalex.org/W4403761038","https://openalex.org/W4404859310"],"related_works":[],"abstract_inverted_index":{"The":[0,55,105,126],"humanization":[1,33],"of":[2,7,18,77,101,113],"antibodies":[3,37,86],"(Abs)":[4],"remains":[5],"one":[6],"the":[8,16,68,72,78,82,99,110,114],"main":[9],"pathways":[10],"for":[11,31],"therapeutic":[12],"antibody":[13,32,116],"development.":[14],"With":[15],"advantages":[17],"diffusion":[19,28],"models,":[20],"here":[21],"we":[22],"present":[23],"HuAbDiffusion,":[24],"a":[25,95],"discrete":[26],"language":[27,103],"model":[29,56],"used":[30],"by":[34,124],"generating":[35],"humanized":[36,85,115],"from":[38,42],"scratch.":[39],"HuAbDiffusion":[40],"starts":[41],"three":[43],"complementary":[44],"determinant":[45],"regions":[46],"(CDRs)":[47],"and":[48,62,74],"finally":[49],"generate":[50],"whole":[51],"V":[52],"region":[53],"sequences.":[54],"was":[57],"evaluated":[58],"on":[59],"22":[60],"mAbs":[61],"compared":[63],"with":[64,98],"several":[65],"existing":[66],"methods,":[67],"test":[69],"results":[70],"show":[71],"effectiveness":[73],"better":[75],"performance":[76],"proposed":[79],"model.":[80],"Besides,":[81],"potential":[83],"optimal":[84],"to":[87,94],"be":[88,91,118,129],"selected":[89],"could":[90],"narrowed":[92],"down":[93],"reasonable":[96],"level":[97],"usage":[100],"pretrained":[102],"models.":[104],"most":[106],"significant":[107],"is":[108],"that":[109],"binding":[111],"affinity":[112],"can":[117,128],"retained":[119],"or":[120],"even":[121],"increased":[122],"generated":[123],"HuAbDiffusion.":[125],"method":[127],"reached":[130],"out":[131],"through":[132],"our":[133],"previous":[134],"established":[135],"YabXnization":[136],"server":[137],"at":[138],"https://www.genscript.com/tools/yabxnization-service.":[139]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-12-11T00:00:00"}