Molecular docking is a vital computational tool used to predict the preferred orientation of a guest molecule within the cavity of host molecules like cyclodextrins. These cyclic oligosaccharides, composed of glucose subunits, possess a unique truncated cone-like structure with a hydrophobic interior and a hydrophilic exterior.

In our recent studies led by @Fanny Beekman, we have utilized various docking algorithms to investigate the binding affinities of different pharmaceutical compounds. Understanding these interactions is crucial for the development of advanced drug delivery systems, where #cyclodextrins serve as carriers to improve the solubility and stability of hydrophobic drugs. By simulating these host-guest complexes, we can gain insights into the thermodynamic favorability and the specific non-covalent interactions, such as van der Waals forces and hydrophobic effects, that drive the inclusion process.