Computational Structural Biology: Winter 2024

Introduction: Bioinformatics vs Computational Structural Biology

Molecular Simulations

A major goal of molecular biology is to understand at the atomic level the function of macromolecules and/or biological nano-machines, which is believed to be intimately related to the dynamics of their structures. Our current understanding of the dynamics of macromolecules is, however, largely incomplete. This arises as only a few experimental techniques are capable of collecting time-resolved structural data, and those that can are usually limited to a narrow time window. The main option to circumvent the limitation of experimental methods is to rely on simulations, with the most popular method in molecular biology being molecular dynamics.

Molecular dynamics (MD) is a computer simulation method for studying the movements of atoms and molecules. The atoms and molecules are allowed to interact, giving a view of the dynamic evolution of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion, where forces between the atoms and their potential energies are calculated using molecular mechanics force fields. The method was originally developed within the field of theoretical physics in the late 1950s but is applied today mostly in chemical physics, materials science and the modelling of biomolecules.

The cycle of simulations