{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T12:52:06Z","timestamp":1791895926137,"version":"4.3.4"},"reference-count":39,"publisher":"Wiley","issue":"9","license":[{"start":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:00:00Z","timestamp":1787529600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:00:00Z","timestamp":1787529600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100004329","name":"Javna Agencija za Raziskovalno Dejavnost RS","doi-asserted-by":"publisher","award":["P1\u20100201"],"award-info":[{"award-number":["P1\u20100201"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004329","name":"Javna Agencija za Raziskovalno Dejavnost RS","doi-asserted-by":"publisher","award":["J1\u201050026"],"award-info":[{"award-number":["J1\u201050026"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Accurate structural data in a standardized format is one of the key factors behind the success of machine learning (ML)\u2010based methods for protein design and structure prediction. However, their application to nanobody\u2010antigen complexes has lower success rates compared to globular protein complexes, partly due to the limited amount of high\u2010quality structural data. While several dedicated databases already exist, automated assembly pipelines frequently overlook various artifacts, which act as additional noise and limit the effectiveness of ML applications. Common issues include incorrectly defined antigen assemblies, redundancy bias, inclusion of crystal contacts, strained geometry due to crystal packing, as well as missing density or post\u2010translational modifications near the interface. To address these issues, we present\n                    <jats:bold>A<\/jats:bold>\n                    ntigen\u2010\n                    <jats:bold>V<\/jats:bold>\n                    HH\n                    <jats:bold>I<\/jats:bold>\n                    nterface\n                    <jats:bold>D<\/jats:bold>\n                    atabase (\n                    <jats:bold>AVIDbase<\/jats:bold>\n                    ), a highly curated dataset of nanobody\u2010antigen structures. In addition to correcting structural artifacts, the dataset provides a nonredundant set of structures with standardized chain identifiers, harmonized metadata, and cleaned atomic coordinates in a ready\u2010to\u2010use format for ML applications. AVIDbase is available on GitHub (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/github.com\/Novartis\/AVIDbase\">github.com\/Novartis\/AVIDbase<\/jats:ext-link>\n                    ) and Zenodo (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/doi.org\/10.5281\/zenodo.20488703\">doi.org\/10.5281\/zenodo.20488703<\/jats:ext-link>\n                    ).\n                  <\/jats:p>","DOI":"10.1002\/pro.70773","type":"journal-article","created":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T11:43:10Z","timestamp":1787571790000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["<scp>AVIDbase<\/scp>\n                    : A biologically accurate structural dataset of nanobody\u2010antigen complexes"],"prefix":"10.1002","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-4022-7068","authenticated-orcid":false,"given":"Tadej","family":"Medved","sequence":"first","affiliation":[{"name":"Biologics Drug Product Development Novartis LLC  Menge\u0161 Slovenia"},{"name":"Faculty of Chemistry and Chemical Technology University of Ljubljana  Ljubljana Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1021-3803","authenticated-orcid":false,"given":"Jurij","family":"Lah","sequence":"additional","affiliation":[{"name":"Faculty of Chemistry and Chemical Technology University of Ljubljana  Ljubljana Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Goran","family":"Mili\u010di\u0107","sequence":"additional","affiliation":[{"name":"Biologics Drug Product Development Novartis LLC  Menge\u0161 Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5615-7918","authenticated-orcid":false,"given":"San","family":"Had\u017ei","sequence":"additional","affiliation":[{"name":"Faculty of Chemistry and Chemical Technology University of Ljubljana  Ljubljana Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,8,24]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07487-w"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-50722-y"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00125"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.5c00410"},{"key":"e_1_2_9_6_1","unstructured":"BennettNR WatsonJL RagotteRJ BorstAJ SeeDL WeidleC et al.Atomically accurate de novo design of antibodies with RFdiffusion.2025BioRxiv 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