Global ligand-protein docking tools: Comparation and Case study

Abstract

Molecular docking study, a method used in drug discovery, is used to estimate the interactions between small molecules and macromolecules. Docking can be divided into rigid and flexible docking where local and global docking is the subclass in the flexible approach. Two important criteria in docking are search algorithms and scoring functions. The former assesses the fitness of ligand poses within the protein’s binding site, while the latter explores different ligands “conformations until the point at which the least energy convergence is achieved.” Three user-friendly global docking programs (AutoDock Vina, MOE, and DOCK6) are utilized to study ligand behaviors against Enterovirus A71 3C protease (3Cpro), which causes hand-foot-mouth disease in children. The results suggested that the DOCK6 gives the fastest output, and all of the ligands correctly bind to the active site of 3Cpro. Rupintrivir is a good candidate for serving as a positive control in all three tools for binding site identification because it shows broad resistance to viruses. In comparison to AutoDock Vina and MOE, DOCK6 exhibits superior conformational space search efficiency and speed across the three docking technologies used in our investigation. AutoDock Vina, however, is typically regarded as being more appropriate for novices.