Molecular docking shows a very important role in the rational design of drugs. Method of molecular docking calculates the preferred orientation of one molecule with the second molecule when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules. Docking is normally used to predict the binding orientation of small molecule drug candidates to their protein targets in order to predict the affinity and activity of the small molecule. Given the biological and pharmaceutical importance of molecular docking, considerable efforts have been directed towards improving the methods used to calculate docking. The docking process simulates the ligand-protein pairwise interaction and the energies are calculated. There are three types of Docking: Protein-Protein Docking, Protein-Ligand Docking and Protein-Protein and Protein-Ligand docking. Molecular docking software includes Auto dock, Flex-X, Glide, Gold, ZDOCK, RDOCK, LeDOCK, Dock, Auto dock Vina, Mdock etc. The present review accumulates the characteristics and applications of the different software used and the basic challenges faced in molecular docking studies.