EMBL Hamburg

Abstract The structural characterisation of protein-protein 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. To address this problem, I developed gapTrick, an AlphaFold2-based approach that uses multimeric templates to improve prediction reliability.

Abstract The structural characterisation of protein-protein interactions is a key step in understanding the functions of living cells. Models of protein complexes provide important insights into interaction mechanisms, but their interpretation can be difficult if they lack fine structural detail, which is often the case in experimental and predicted models.

Abstract AlphaFold 3 has significantly advanced the modeling of macromolecular structures, including proteins, DNA, RNA, and their interactions with small molecules or post-translational modifications. However, challenges remain when modeling specific structural conformations or complexes with limited evolutionary data, such as protein-antibody complexes.