Experimentally derived protein structures and predicted structures often require certain structure improvement and refinement in order to bring them closer to real in vivo working conformations. When a structure is prepared in a molecular modelling software package, the initial geometry does not necessarily correspond to one of the stable conformers. Therefore, energy minimization is usually carried out to determine a stable conformer which involves finding the geometry of a particular arrangement of the atoms that represents a local or global energy minimum. The procedure involves finding a minimum on the potential energy surface starting from a higher energy initial structure. This process is also termed as geometry optimization.
Energy minimization procedure involves changing the geometry in a stepwise manner so that the energy of the molecule is reduced and after a number of steps, a local or global minimum on the potential energy surface is reached. Some of the commonly used energy minimization methods are Steepest Descent method, Conjugate Gradient method and Newton-Raphson method. You can read more about them in detail here.
Structure Optimisation/Energy Minimization was used in the following examples: