AA-Score: a New Scoring Function Based on Amino Acid Specific Interaction for Molecular Docking

The protein-ligand scoring function plays an important role in computer-aided drug discovery, which is heavily used in virtual screening and lead optimization. In this study, we developed a new empirical protein-ligand scoring function, which is a linear combination of empirical energy components, including hydrogen bond, van der Waals, electrostatic, hydrophobic, π-stacking, π-cation, and metal-ligand interaction. Different from previous empirical scoring functions, AA-Score uses several amino acid-specific empirical interaction components. We tested AA-Score on several test sets. The resulting performance shows AA-Score performs well on scoring, docking, and ranking compared with other widely used traditional scoring functions. Our results suggest that AA-Score gains substantial improvements from using detailed protein-ligand interaction components. Besides, we developed an easy-to-use tool to analyze protein-ligand interaction fingerprint and predict binding affinity using AA-Score.