Molecular docking, estimating free energies of binding, and AutoDock’s semi-empirical force field

Discussions and questions about methods, approaches, and tools for estimating (relative) binding free energies of protein-ligand complexes are quite popular, and even the simplest tools can be quite tricky to use. Here, I want to briefly summarize the idea of molecular docking, and give a short overview about how we can use AutoDock 4.2’s hybrid approach for evaluating binding affinities.