In the enzymology, the palmitoyl – co a hydrolase is said to the enzyme that hydrolase the fatty acid. For this enzyme polmitoyl – coa and water are considered. According to available reports this enzymes are effective in regulating of intracellular concentration of acyl coa, fatty acid and co enzyme. Beside the design and construction of effective inhibitors for disabling of enzyme, the study of interaction of enzyme on the inhibitor by using of computational methods in presenting the acceptance model for performance. In the present study the effectiveness of inhibitors named Ibuprofen, Niacin, FMN. On the palmitoyl – co a hydrolase by codes of 3.1.2.2 and by using of dynamics. Molecular computational were simulated and were studied. Simulation in the condition that was similar to the physiological condition in the aquatic environment the temperature of 37 and the pressure of 1 atmosphere was conducted. Then doing the required parameters molecular dynamic from trajectory and extraction simulation and analyzing of results were done. FMN by reducing of irregular rate of RMSD and increasing of accessible level of solvent, regular structures of alpha and Beta are weakest inhibitor were recognized.
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