METHOD OF USING A WATER-BASED PHARMACOPHORE

摘要

A method for producing a template of a binding site of a target protein is provided. A target protein is modeled in silico. A binding site is hydrated with water molecules by finding areas within the binding site where water molecules remain localized during a molecular dynamic simulation. Interactions of the water molecules with the hydration sites are classified as a hydrogen bond acceptor interaction (A) or a hydrogen bond donor interaction (D). The classified interactions are mapped to provide a template of hydrogen bond interactions with the protein.