{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T08:25:32Z","timestamp":1773131132415,"version":"3.50.1"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2025,9,23]],"date-time":"2025-09-23T00:00:00Z","timestamp":1758585600000},"content-version":"vor","delay-in-days":22,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013060","name":"European Molecular Biology Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The structural characterization of protein\u2013protein interactions is a key step in understanding the functions of living cells. Here, I show that AlphaFold3 often fails to predict protein complexes that are either weak or dependent on the presence of a cofactor that is not included in a prediction.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To address this problem, I developed gapTrick, an AlphaFold2-based approach that uses multimeric templates to improve prediction reliability. I demonstrate that gapTrick improves predictions of weak and incomplete complexes based on low-accuracy templates, such as individual protein models that have been rigid-body fitted into cryo-EM reconstructions. I also show that gapTrick identifies residue\u2013residue interactions with high precision. These interaction predictions are a very strong indicator of model correctness. The approach can aid in the interpretation of challenging experimental structures and the computational identification of protein\u2013protein interactions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The gapTrick source code is available at https:\/\/github.com\/gchojnowski\/gapTrick and requires only a standard AlphaFold2 installation to run. The repository also provides a Colab notebook that can be used to run gapTrick without installing it on the user\u2019s computer.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf532","type":"journal-article","created":{"date-parts":[[2025,9,23]],"date-time":"2025-09-23T12:48:51Z","timestamp":1758631731000},"source":"Crossref","is-referenced-by-count":1,"title":["gapTrick\u2014structural characterization of protein\u2013protein interactions using AlphaFold"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3796-8352","authenticated-orcid":false,"given":"Grzegorz","family":"Chojnowski","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, Hamburg Unit , Hamburg 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