The molecular docking approach can be used to model the interaction between a small
molecule and a protein at the atomic level, which allow us to characterize the behavior of
small molecules in the binding site of target proteins as well as to elucidate fundamental
biochemical processes [19]. The docking process involves two basic steps: prediction of the
ligand conformation as well as its position and orientation within these sites (usually
referred to as pose) and assessment of the binding affinity. These two steps are related to
sampling methods and scoring schemes, respectively, which will be discussed in the theory
section.