Docking is the process by which two molecules fit together in 3D space. Docking is a
method which predicts the preferred orientation of one molecule to a second when
bound to each other to form a stable complex. Docking is frequently used to predict
the binding orientation of small molecule drug candidates to their protein targets in
order to in turn predict the affinity and activity of the small molecule. Hence docking
plays an important role in the rational design of drugs. Molecular docking may be
defined as an optimization problem, which would describe the “best-fit” orientation of
a ligand that binds to a particular protein of interest.
The focus of molecular docking is to computationally stimulate the molecular
recognition process. The aim of molecular docking is to achieve an optimized
conformation for both the protein and ligand and relative orientation between protein
and ligand such that the free energy of the overall system is minimized.