Protein and ligand molecules as two separate entities appear and behave differently, but what happens when they come together and interact with each other is one of the interesting facts in modern molecular biology and molecular recognition. This interaction can be well explained with the concept of docking which in a simple way can be described as the study of how a molecule can bind to another molecule to result in a stable entity. The two binding molecules can be either a protein and a ligand or a protein and a protein. Irrespective of which two molecules are interacting, a docking process invariably includes two steps—conformational search through various algorithms and scoring or ranking. Even though prolific research has been carried out in this field, yet it is still a topic of current interest as there is a scope for improvement to rationalize binding interactions with biological function using docking program. This chapter focuses on how to set up and perform docking runs using freeware and commercial software. Most of the known docking protocols like induced fit docking, protein–protein docking, and pharmacophore-based docking have been discussed. The use of pharmacophore queries as filters in virtual screening is also demonstrated using suitable examples.