Explicit Treatment of Water Molecules in Protein-Ligand Docking

No biological process can be fully described by computational techniques unless water is taken into consideration. Unfortunately, accurate representation of the water environment in any biological process is normally too time-consuming with present techniques. Commonly, in ligand-binding docking, all water molecules are removed from the experimental structure data before the system is prepared, in which case it is assumed that all water effects are included in the scoring function. However, many scientific studies include particular water molecules explicitly, following chemical intuition. The choice of the number of water molecules and their positions depends substantially on the problem to be tackled and the information available about the problem. However, not much has been published comparing the quality of docking results with and without water molecules. This paper reviews those docking studies in which the effect of the inclusion of water molecules is analyzed in a large set of compounds. Explicit water molecules can be added to the system in different ways. The most popular option consists of including some water molecules already observed in crystal structures. However, tightly bound water molecules in a protein-ligand complex may not be conserved in complexes with other ligands. This problem can be tackled by coupling the prediction of water molecules with the docking calculation. Programs in which this feature is included are reviewed.