Understanding the structure and dynamics of protein and interaction of proteins with ligands both in aqueous and non-aqueous solutions can be done by many experimental techniques such as X-ray scattering methods, differential scanning colorimetry, differential scanning fluorimetry, circular dichroism spectroscopy, NMR and many other methods.
One of the complimentary method for experimental techniques is molecular modelling. In order to understand the structure and dynamics of proteins, binding of ligands to enzymes, protein-protein interaction and many other properties of proteins in solution molecular modelling methods are very important because they can give molecular level information.
There are many molecular modelling approaches which are based on stochastic or deterministic phenomenon. In this talk few molecular modelling methods such as quantum chemical calculations (QM), Molecular Mechanics methods, Classical Molecular Dynamics (MD) Simulations, Hybrid QM/MM (quantum mechanics/molecular mechanics) and Monte Carlo simulations of proteins will be discussed briefly and some examples of applications of these methods will be introduced.