{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T07:00:25Z","timestamp":1790146825034,"version":"4.0.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["25-75-30013"],"award-info":[{"award-number":["25-75-30013"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>We present a significant update to VDJdb, introducing substantial enhancements to both the data content and the technical infrastructure. The integration of steadily accumulating T-cell receptor (TCR):epitope recognition data, together with advances in high-throughput experimental techniques, has expanded the landscape for machine learning-based prediction of TCR specificity, covering foreign antigens, neoantigens, and autoimmunity-associated epitopes. However, these advances have introduced new challenges, most notably in data quality\u2014large-scale assays have heightened concerns about measurement reliability and exacerbated existing issues such as HLA and epitope coverage biases. To address these issues, we have adopted state-of-the-art artificial intelligence approaches, including protein sequence embeddings and AI-driven structure prediction. The updated VDJdb resource now features TCR specificity records annotated with embedding-derived paratope features, advanced noise filtering capabilities, and predicted three-dimensional protein structures. These improvements enable more comprehensive interrogation of TCR\u2013epitope recognition and provide novel lines of evidence to support the reliability of high-throughput assay records, which are frequently limited by insufficient independent validation. VDJdb can be accessed at https:\/\/vdjdb.com and https:\/\/github.com\/antigenomics\/vdjdb-db.<\/jats:p>","DOI":"10.1093\/nar\/gkag904","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T11:40:37Z","timestamp":1790077237000},"source":"Crossref","is-referenced-by-count":0,"title":["VDJdb in 2026: boosting T-cell receptor recognition evidence using paratope embeddings and AI-based structure prediction"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4993-8636","authenticated-orcid":false,"given":"Daniil V","family":"Luppov","sequence":"first","affiliation":[{"name":"Institute of Translational Medicine, Russian National Medical State University , 117513 Moscow ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-3181-8235","authenticated-orcid":false,"given":"Anna E","family":"Koneva","sequence":"additional","affiliation":[{"name":"Institute of Translational Medicine, Russian National Medical State University , 117513 Moscow ,","place":["Russia"]},{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS , 117997Moscow ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9655-7986","authenticated-orcid":false,"given":"Dmitry V","family":"Bagaev","sequence":"additional","affiliation":[{"name":"BIASlab, Department of Electrical Engineering, Eindhoven University of Technology , 5600 MBEindhoven ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasiia V","family":"Alexandrova","sequence":"additional","affiliation":[{"name":"Institute of Translational Medicine, Russian National Medical State University , 117513 Moscow ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizaveta K","family":"Vlasova","sequence":"additional","affiliation":[{"name":"Institute of Translational Medicine, Russian National Medical State University , 117513 Moscow ,","place":["Russia"]},{"name":"ITMO University , 197101Saint-Petersburg ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0430-790X","authenticated-orcid":false,"given":"Dmitry M","family":"Chudakov","sequence":"additional","affiliation":[{"name":"Institute of Translational Medicine, Russian National Medical State University , 117513 Moscow ,","place":["Russia"]},{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS , 117997Moscow ,","place":["Russia"]},{"name":"Center for Molecular and Cellular Biology , 121205Moscow ,","place":["Russia"]},{"name":"Abu Dhabi Stem Cells Center (ADSCC) , 00000Abu Dhabi ,","place":["United Arab Emirates"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9027-742X","authenticated-orcid":false,"given":"Chihiro","family":"Motozono","sequence":"additional","affiliation":[{"name":"Division of Human Molecular Immunology, Joint Research Center for Human Retrovirus Infection, Kumamoto University , 860-0811Kumamoto ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3194-3135","authenticated-orcid":false,"given":"Andrew K","family":"Sewell","sequence":"additional","affiliation":[{"name":"Division of Human Molecular Immunology, Joint Research Center for Human Retrovirus Infection, Kumamoto University , 860-0811Kumamoto ,","place":["Japan"]},{"name":"Division of Infection and Immunity, Cardiff University School of Medicine , CF14 4XNCardiff, Wales ,","place":["United 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