AutoDock is a molecular modeling simulation software designed for protein-ligand docking, a technique to predict the position and orientation of a ligand (a small molecule) when it is bound to a protein receptor or enzyme.
AutoDock Vina is an improved version has an improved local search routine that makes use of multicore/multi-CPU computer setups. AutoDock Vina tends to be faster than AutoDock 4 by orders of magnitude.
In a recent study both software were tried on 800 protein–ligand complexes for which both PDB structures and experimental binding affinity are available. The title of the paper gives a brief summary “Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity” (Nguyen et al. J. Chem. Inf. Model. 2020, 60, 1, 204–211.)