Fig. 1. Our model architecture. A protein–ligand complex is represented in a graph and adjacency matrices are assigned from the binding structure of the complex. Each node feature is updated through neural networks to carry the information of covalent bonds and intermolecular interactions. Given the distance and final node features of each atom pair, four energy components are calculated from the physics-informed parameterized equations. The total binding affinity is obtained as a sum of pairwise binding affinities, which is a sum of the four energy components divided by an entropy term.
