CHAPTER 13: Protein–Ligand Docking

Docking is the process by which structural data from X-ray crystallography is used to predict the binding modes of ligands in protein binding sites without the need to conduct crystallography experiments. Much progress has been made in the development of tools that will fulfil this dream, and importantly an understanding of when and where docking should be used to best effect and understand the probabilities of success. This chapter covers the concepts of docking from the search algorithms to the scoring functions. One of the more popular algorithms used in industry and academia is introduced, GOLD: Genetic Optimisation for Ligand Docking. Lastly, there is a discussion of how docking can be best used to improve the probability of success in prospective studies.