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The liver plays a central role in transforming and clearing chemicals which is susceptible to the toxicity from agents. Hepatotoxicity is the capacity of a drug or chemical to produce injury to the liver. Agents with recognized hepatotoxicity include carbon tetrachloride, alcohol . The study was focused to investigate the comparative effect of ethanolic extracts of Justicia adhatoda, Mimosa pudica and Vitex negundo on hepatoprotective activity against Perchloroethylene induced liver damage in albino rats both in vitro and in vivo evaluation. The functional properties of target proteins responsible for liver cancer were studied and comparative modeling of target proteins was attempted for high percent sequence identity for structural homology. Modeled protein was modeled with natural and synthetic compounds in order to find the preferred orientation and binding affinity of drug with target protein using scoring functions.