Molecular dynamics simulations have been successfully incorporated and evolved into a mature technique within a variety of pharmaceutical research programs to study the complex biological and chemical systems. Broadly used in modern drug design, molecular docking methods can be used effectively to understand the macromolecular structure-to-function relationships and ligand conformations adopted within the binding sites of macromolecular targets. Information gathered about the dynamic properties of ligand–receptor binding such as free energy by evaluating critical phenomena involved in the intermolecular recognition process. These results can be employed to shift the usual paradigm of structural bioinformatics from studying single structures to analyse conformational ensembles. Today, as a variety of docking algorithms are available, an understanding of advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this chapter is to examine the current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advancements in the field and role played by integration of structure-and ligand-based methods
