web server. The aptamer will most likely attach to this binding site as well. It highlighted the most significant areas of the graph, which also shows the likely site for aptamer binding. Critical atomic interactions and structural properties are learned by the GNN to predict the binding location. To validate this, the binding site on the HER2 surface was estimated using a machine-learning method known as P2Rank . It predicts the ability to bind ligands on the HER2 surface, or ligandability.