Enhancing PROTAC ternary complex prediction with ligand information in AlphaFold 3

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In this study, we assess the capabilities of AlphaFold 3 (AF3) for modeling ligand-mediated ternary complexes, focusing on PROteolysis-TArgeting Chimeras (PROTACs). We demonstrate that when ligand information is provided, AF3 achieves high structural accuracy, even for post-2021 structures that were not included in its training set.

Recommended citation: Erazo, Francisco et al. (2025) “Enhancing PROTAC ternary complex prediction with ligand information in AlphaFold 3.” ChemRxiv.