Methods for docking small molecules to macromolecules: a user's perspective. 2. Applications.

A large number of research articles describe novel methodologies of docking and/or scoring methods. An even larger number of publications report the successful use of these methods in the identification of novel hit molecules. What is less documented is the application of docking methods in other areas. We review herein the application of docking methods to not only hit identification but also to de novo design, fragment-based drug discovery, lead optimization, metabolism prediction, off-target binding, selectivity, protein structure prediction and drug-drug interaction.