[...] it's wise to choose this protein as the target to come up with HCV inhibitors. The cost that is involved in the research and development of a new anti-viral drug is very high to be afforded by the developing countries.[...] plant based products such as flavonoids have been selected based on their known effects and its specificity and then it is screened to check the efficacy. 2.2 Selection of compounds From the list of selected plants using the criteria mentioned above, the flavonoids that were reported in these plants were searched in online tools using search engines such as NCBI, BMC, Science Direct, Google patent search, Herbalgram. org etc. 2.3 Docking Studies Molecular docking of the flavonoids with NS3 protease is done by the following steps: 2.3. 1 Preparation of Ligands The 2D structure of each flavonoid selected was drawn using Chem Draw software and was saved as a MOL file. About 50 flavonoids showed the affinity of<-7 kcal/mol 3.3 Ligplot Analysis of the Lead Molecules These lead molecules were viewed on ligplot software to study about the interactions of these molecules with the protease 3.4 MD Simulation Results Oligomeric Proanthocyanadins and Quercitroside were chosen as the positive control with binding affinity of-9.3 kcal/mol and 5, 7-Dihydroxy-3-methoxy-8-methylflavone with binding affinity of-5.8 kcal/mol as negative control was chosen for MD simulation studies. 5, 7-Dihydroxy-3methoxy-8-methylflavone showed better interactions than Oligomeric Proanthocyanadins and Quercitroside. 1016 analogs of 5, 7-Dihydroxy-3-methoxy-8-methylflavone was searched in PubChem and again docked individually against NS3 protease.