Chapter 20 – Computational Tools for the Study of Biomolecules

Abstract Chemistry is not alien to the scientific revolution triggered by the generalization of the usage of computers. Quite probably, the area where the ensuing changes have been more notorious is physical chemistry and, in particular, the analysis of the energetic and dynamic aspects of the molecular systems. Numerical simulations of structural changes and chemical/biochemical processes in such systems have become accurate enough to complement the experimental studies and to shed light on the laboratory observations. In the present chapter, we aim to provide a general description of the methods used to simulate systems of biological interest, which range from relatively small drugs formed by tens of atoms to DNA fragments, proteins, and enzymes formed by millions of atoms. Our presentation will first concentrate on the different approaches to calculate the energy of a system for a certain nuclear configuration, which serve as starting point for the dynamic methodologies that study its time evolution, described in the second moiety of the chapter. Our goal is not to present a careful and detailed discussion of all the material covered in the chapter, which would consist of not one but several books, but to provide a general overview of the field and the key references necessary to deepen the study of any of its parts.