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Creating a new molecular description factor based on the results of computational docking study will add new dimensions in molecular evaluation. We propose a new molecular description factor analysis system named comparative molecular interaction profile analysis system (CoMIPA) in which the AutoDock program is used for docking evaluation of small molecule compound-protein complexes. Interaction energies are calculated, and the data sets obtained are named interaction profiles (IPFs). Using IPF as a scoring indicator, the system could be a powerful tool to cluster the interacting properties between small molecules and bio macromolecules such as ligand-receptor bindings. The system can use computational molecular docking results to explain biological events such as adverse drug reactions and possibly other unforeseen interactions caused by environmental hormones. We believe that the system has the potential to be a major stepping-stone for bridging computational science and biology.