Pairwise input neural network for target-ligand interaction prediction

Prediction the interactions between proteins (targets) and small molecules (ligands) is a critical task for the drug discovery in silico. In this work, we consider the target binding site instead of the whole target and propose a pairwise input neural network (PINN) for constructing the site-ligand interaction prediction model. Different with the ordinary artificial neural network (ANN) with one vector as input, the proposed PINN can accept a pair of vectors as the input, corresponding to a binding site and a ligand respectively. The 5-CV evaluation results show that PINN outperforms other representative target-ligand interaction prediction methods.