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As the information era dawns, computer aided drug design has become an indispensable component in current drug industries. Many good works have done using computer aided drug design tools. As more and more efforts have been put into the discovery of anti-HIV drugs, our investigation interesting has been focused on the anti-HIV drug design. In our study of anti-HIV inhibitor design, we have obtained a number of significant achievements by incorporating miscellaneous modules of different drug design software's with HIV protease (HIV Pr) as the main target. Furthermore, we also applied computer aided drug design tools to other anti-virus investigations, such as SARS and H5N1 influenza virus. Some significant results have been gained, which are useful for the anti-virus inhibitor design in future.