AlphaFold3 (aka AF3) is an advanced AI model developed by DeepMind for predicting the 3D structures of proteins, nucleic acids, small molecules, and post-translational modification with high accuracy. It supports multi-chains and therefore is also a cofolding or docking method.
DiffDock is a diffusion-based ML model for the docking of a protein to a small molecule. DiffDock reports a confidence score (-inf, inf) where a larger number is better, and scores below -1.5 can be considered low confidence. Note the confidence score does not predict the affinity, aka strength of the biochemical attraction, of the complex.
Molecular docking predicts how molecular structures, such as proteins and ligands, interact to form stable complexes. This process has been challenging in drug design and molecular biology, often requiring extensive computational methods.