Performance of protein-ligand docking with CDK4/6 inhibitors: A case study

Abstract

It is widely believed that tertiary protein-ligand interactions are essential in determining protein function. Currently, the structure sampling and scoring function in traditional docking methods still have limitations. Therefore, new methods for protein-ligand docking are desirable. The accurate docking can speed up the early-stage development of new drugs. Here we present a multi-source information-based protein-ligand docking approach (pmDock). In the CDK4/6 inhibitor case study, pmDock produces a substantial accuracy increases between the predicted geometry centers of ligands and experiments compared to AutoDock and SwissDock alone. Also, pmDock improves predictions for critical binding sites and captures more tertiary binding interactions. Our results demonstrate that pmDock is a reliable docking method for accurate protein-ligand prediction.