{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T01:43:24Z","timestamp":1775958204235,"version":"3.50.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2025,7,31]],"date-time":"2025-07-31T00:00:00Z","timestamp":1753920000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Division of General Medical Sciences"},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ovarian Cancer Institute"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Accurate structures of protein complexes are essential for understanding biological pathway function. A previous study showed how downstream modifications to AlphaFold 2 could yield AF2Complex, a model better suited for protein complexes. Here, we introduce AF3Complex, a model equipped with both similar and novel improvements, built on AlphaFold 3.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Benchmarking AF3Complex and AlphaFold 3 on a large dataset of protein complexes, it was shown that AF3Complex outperforms AlphaFold 3. Moreover, by evaluating the structures generated by AF3Complex on datasets of protein\u2013peptide complexes and antibody\u2013antigen complexes, it was established that AF3Complex could create high-fidelity structures for these challenging complex types. Additionally, when deployed to generate structural predictions for protein complexes used in the recent CASP16 competition, AF3Complex yielded structures that would have placed it among the top models in the competition.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The AF3Complex code is freely available at https:\/\/github.com\/Jfeldman34\/AF3Complex.git.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf432","type":"journal-article","created":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:53:48Z","timestamp":1753876428000},"source":"Crossref","is-referenced-by-count":10,"title":["AF3Complex yields improved structural predictions of protein complexes"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4130-6447","authenticated-orcid":false,"given":"Jonathan","family":"Feldman","sequence":"first","affiliation":[{"name":"Center for the Study of Systems Biology\/School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332,","place":["United States"]},{"name":"School of Computer Science, Georgia Institute of Technology , Atlanta, GA 30332,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1877-4958","authenticated-orcid":false,"given":"Jeffrey","family":"Skolnick","sequence":"additional","affiliation":[{"name":"Center for the Study of Systems Biology\/School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332,","place":["United 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