{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T20:32:49Z","timestamp":1778272369819,"version":"3.51.4"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2019,10,7]],"date-time":"2019-10-07T00:00:00Z","timestamp":1570406400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["17-15-01495"],"award-info":[{"award-number":["17-15-01495"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Here, we report an update of the VDJdb database with a substantial increase in the number of T-cell receptor (TCR) sequences and their cognate antigens. The update further provides a new database infrastructure featuring two additional analysis modes that facilitate database querying and real-world data analysis. The increased yield of TCR specificity identification methods and the overall increase in the number of studies in the field has allowed us to expand the database more than 5-fold. Furthermore, several new analysis methods are included. For example, batch annotation of TCR repertoire sequencing samples allows for annotating large datasets on-line. Using recently developed bioinformatic methods for TCR motif mining, we have built a reduced set of high-quality TCR motifs that can be used for both training TCR specificity predictors and matching against TCRs of interest. These additions enhance the versatility of the VDJdb in the task of exploring T-cell antigen specificities. The database is available at https:\/\/vdjdb.cdr3.net.<\/jats:p>","DOI":"10.1093\/nar\/gkz874","type":"journal-article","created":{"date-parts":[[2019,9,30]],"date-time":"2019-09-30T03:17:51Z","timestamp":1569813471000},"page":"D1057-D1062","source":"Crossref","is-referenced-by-count":401,"title":["VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium"],"prefix":"10.1093","volume":"48","author":[{"given":"Dmitry V","family":"Bagaev","sequence":"first","affiliation":[{"name":"Pirogov Russian Medical State University, Moscow, Russia"},{"name":"Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia"}]},{"given":"Renske M A","family":"Vroomans","sequence":"additional","affiliation":[{"name":"Origins Center, Groningen, The Netherlands"},{"name":"Institute for Advanced Study, University of Amsterdam, Amsterdam, The Netherlands"}]},{"given":"Jerome","family":"Samir","sequence":"additional","affiliation":[{"name":"Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, Australia"},{"name":"School of Medical Sciences, UNSW Sydney, Sydney, Australia"}]},{"given":"Ulrik","family":"Stervbo","sequence":"additional","affiliation":[{"name":"Center for Translational Medicine, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany"},{"name":"Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, Corporate Member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, Berlin, Germany"}]},{"given":"Cristina","family":"Rius","sequence":"additional","affiliation":[{"name":"Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK"}]},{"given":"Garry","family":"Dolton","sequence":"additional","affiliation":[{"name":"Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, 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Bochum, Herne, Germany"},{"name":"Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, Corporate Member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, Berlin, Germany"}]},{"given":"David K","family":"Cole","sequence":"additional","affiliation":[{"name":"Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK"},{"name":"Immunocore Ltd., Abingdon, OX14 4RY, UK"}]},{"given":"Andrew J","family":"Godkin","sequence":"additional","affiliation":[{"name":"Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK"}]},{"given":"Andrew K","family":"Sewell","sequence":"additional","affiliation":[{"name":"Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK"}]},{"given":"Can","family":"Kesmir","sequence":"additional","affiliation":[{"name":"Theoretical Biology and Bioinformatics Department, Science Faculty, Utrecht University, Utrecht, Netherlands"}]},{"given":"Dmitriy M","family":"Chudakov","sequence":"additional","affiliation":[{"name":"Pirogov Russian Medical State University, Moscow, Russia"},{"name":"Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia"},{"name":"Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia"}]},{"given":"Fabio","family":"Luciani","sequence":"additional","affiliation":[{"name":"Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, Australia"},{"name":"School of Medical Sciences, UNSW Sydney, Sydney, Australia"}]},{"given":"Mikhail","family":"Shugay","sequence":"additional","affiliation":[{"name":"Pirogov Russian Medical State University, Moscow, Russia"},{"name":"Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia"},{"name":"Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 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