Accurate structure prediction of biomolecular interactions with AlphaFold 3
This paper introduced AlphaFold 3, a unified deep learning model that predicts the joint structure of complexes containing proteins, nucleic acids, small-molecule ligands, ions, and modified residues. It replaces much of the prior architecture with a diffusion-based module that directly generates atomic coordinates. The model achieved substantially improved accuracy over specialized tools across many interaction types, including protein-ligand and protein-nucleic acid complexes.