• CS-PD: Proteins were described by domains and ligands were represented by substructures in CS-PD model. Sparse canonical correspondence analysis (SCCA) algorithm was applied to recognize the physical-chemical factors between the domains and substructures. In prediction phase, the domain and substructure physical-chemical factors in a given target-ligand pair were added to generate a discriminant value. If the value was higher than a threshold, the target and ligand were predicted to interact with each other.