Computational approaches are roughly categorized into two groups: structure-based and structure-free (chemical genomics-based) methods. Structure-based methods evaluate CPIs by calculating physical chemistry-based scores from three-dimensional (3D) complex models generated by molecular docking simulations . When reliable 3D structures of the target proteins are available, docking methods can be applied without prior information on known interactions. The performance is heavily dependent on the accuracy of the scoring function and predicted docking pose. Structure-free methods are primarily chemoinformatic approaches that utilize prior information on known CPIs to predict unknown interactions. They can accurately predict CPIs with relatively low computational costs when the prior information covers a sufficient pharmacological space.