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Molecular docking is a computational method to study the formation of intermolecular complexes of one small molecule ligand (drug lead) with a macromolecule, which usually is a protein (drug target) of known three dimensional structure. Four different types of interactions between the molecules can be distinguished such as 1) protein-protein; 2) protein-DNA; 3) DNA-ligand and 4) protein-ligand. In recent years, the availability of three dimensional (3D) structures for many macromolecular drug targets (proteins) and rapid advancement in computational chemistry and bioinformatics, both in vitro and in silico serve a new novel platform for the development as well as exploring modern computational methods. When the 3 D structure of the macromolecular target is known, then the design of the computational library can be customized to suit the geometry of the binding site. Moreover, identifying binding sites and protein-ligand interactions using bioinformatics tools before venturing into wet laboratory studies saves the energy, time and money considerably.