A computer-implemented method of training a machine learning model to learn ligand binding similarities between protein binding sites is disclosed. The method comprises inputting to the machine learning model: a representation of a first binding site; a representation of a second binding site, wherein the representations of the first and second binding sites comprise structural information; and a label comprising an indication of ligand binding similarity between the first binding site and the second binding site. The method also comprises outputting from the machine model a similarity indicator based on the representations of the first and second binding sites; performing a comparison between the similarity indicator and the label; and updating the machine learning model based on the comparison.