Improving AlphaFold 3 structural modeling by incorporating explicit crosslinks

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. Previous studies with AlphaFold2 demonstrated that adding distance restraints from crosslinking mass spectrometry (XL-MS) can improve predictions for such cases. In this study, we investigate whether XL-MS restraints can be incorporated into AlphaFold 3 by explicitly modeling crosslinks as covalently-bound ligands. Our results show that this approach is able to increase the accuracy of AlphaFold 3 models. We explore the opportunities and limitations of this method, which has been implemented as a proof-of-concept pipeline named AlphaFold 3x, available at<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/KosinskiLab/alphafold3x">https://github.com/KosinskiLab/alphafold3x</ext-link>.