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Structural based drug design has been widely used in drug discovery for leading compounds identification and optimization.Many successful applications have been reported.Various docking methods and de novo structural based drug design programs have been developed,which were all developed based on the single target binding assumption.However,drugs encounter complicated situations and a huge number of biological molecules in the human body and may cause unexpected deleterious or beneficial effects.In order to understand mechanism of drug action,disease related molecular networks need to be studied.