Molecular interaction is the basis for protein and cellular function. Careful
inhibition or modulation of these is the main goal of therapeutic compounds. In the
pharmaceutical field, this process is referred to as pharmacodynamics. Over the years,
there have been several hypotheses attempting to describe this complex phenomenon.
From a purely biophysical point of view, molecular interactions may be attributed to
pairwise contributions such as charge angles, torsions, and overall energy. Thus, the
computation of binding affinity is possible, at least in principle. Over the last half of the
past century, molecular simulation was developed using a combination of physics,
mathematics, and thermodynamics. Currently, these methods are known as structure-based drug design (SBDD) and it has become a staple of computer-aided drug design
(CADD). In this chapter, we present an overview of the theory, current advances, and
limitations of molecular dynamics simulations. We put a special focus on their
application to virtual screening and drug development.
Keywords: Drug Design, Enhanced Sampling, Molecular Interaction, Molecular Simulation.
