Editing Protein engineering (section)

====''Ab initio''====
These methods involve free modeling without using any structural information about the template. ''Ab initio'' methods are aimed at prediction of the native structures of proteins corresponding to the global minimum of its free energy. some examples of ''ab initio'' methods are AMBER, GROMOS, GROMACS, CHARMM, OPLS, and ENCEPP12. General steps for  ''ab initio'' methods begin with the geometric representation of the protein of interest. Next, a potential energy function model for the protein is developed. This model can be created using either molecular mechanics potentials or protein structure derived potential functions. Following the development of a potential model, energy search techniques including molecular dynamic simulations, Monte Carlo simulations and genetic algorithms are applied to the protein.<ref name=PoluriBook/>{{page needed|date=May 2017}}