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The molecularly imprinted polymers (MIPs) development is an efficient system that can be used to create binding sites for template molecules that take into account the test molecules' size, shape, and functional groups. Presently, knowledge of the interaction of MIPs as Systems for recognizing hosts-guests is limited. In the present study, we screened out different monomers IA, MAA, and AMPSA and their Insilco interaction with cyanotoxin to evaluate the possibility of developing MIP-based biosensors. By using Insilco computational tools monomers were designed and screened against toxins. To examine their interaction with the template, the highest affinity monomers were chosen and employed in a simulated annealing procedure. The generation of MIPs and their attributes can both be demonstrated using this low-cost computational method.