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Molecular dynamics can be used to simulate the time evolution of microscopic system. Biological systems like DNA, lipid membranes and, most importantly, proteins have been intensively studied using these techniques. The various steps involved in molecular dynamics simulations of proteins will be presented, together with their applications to biological phenomenon. In particular, results of simulations performed on important proteins of the immune system will be given and how these data can be used to optimize cancer treatment will be shown.