Development of a new docking method using the hypothetical hydratedligand which take account of bridging water molecules

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In protein-ligand docking methods, the interaction of the target protein with the ligand molecule through water is rarely considered. In the formation of protein-ligand complex, however, there are some cases that water molecules play a significant role in stabilizing the protein-ligand interactions by hydrogen-bond bridging between the protein and the ligand. In this study, we devise the easy-to-use docking approach using the hypothetical hydrated ligand which take account of water molecules involving in recognition of the ligand by the protein and stabilizing the protein -ligand interactions.