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Abstract: The quality of molecularly imprinted polymers depends on the ability to form molecule-specific recognition sites within the host gel. We investigate the imprinting quality of cross-linked polymer networks using molecular dynamics simulations through a topological analysis of the imprinted network configuration before and after removal of the templates. We define a measure for the quality of the imprinted polymer on the basis of the shape and size of the imprinting-induced binding sites. Low qualities of the imprinted gels are attributed to aggregation of the templates in the prepolymerization solution, aggregation of the imprinting-induced sites with small pores inherent to the gel, and deformation of the binding sites due to relaxation of the gel after removal of the templates. The formation of distinct individual cavities that retain the size and shape of the template is enhanced by high degrees of cross-linking and low template concentrations, in agreement with experimental observations.