Computer Modelling and Molecular Dynamics Simulation of Biomolecules

Molecular modelling and molecular simulation approaches are increasingly being used in many areas of biochemistry as well as structural and molecular biology. These techniques can be extremely helpful to model the structure of biomolecules and to investigate the structural dynamics and how it is coupled to biomolecular function. However, understanding the physical basis of molecular modelling and the principles of computer algorithms to perform simulations is of great importance in order to apply these techniques and to appropriately analyse and interpret the results. The present chapter contribution provides a solid basis for understanding the physical principles of molecular simulations and gives an overview on the most important approaches to extract structural and thermodynamic quantities. Useful approximations such as implicit solvent and coarse-grained modelling are covered to extend the applicability to large biomolecular structures. Limitations and approximations associated with each technique are discussed. The chapter also includes applications of molecular simulations for predicting protein structures and to calculate the effect of mutations on biomolecular binding.