Molecular imprinting is an established method for the creation of artificial recognition sites in synthetic materials through polymerization and cross-linking in the presence of template Molecules. Removal of the templates leaves cavities that are complementary to the template molecules in size, shape, and functionality. Although this technique is effective when targeting small molecules, attempts to extend it to larger templates, such as proteins, have failed to show similar success. As opposed to small molecules, proteins are characterized by large size, flexible Structure, and large number of functional groups available for recognition, which make it impossible to use imprinting protocols of small molecules for protein imprinting. In this research We use lattice Monte Carlo simulations of an imprinting process using radical polymerization of hydrogels as a simple model for potein-imprinted polymers (PIPs). We investigate the properties of the resulting polymer gel by studying the effects of initiator, cross-linker, and monomer concentrations and the presence of protein on gel Structure and porosity. The Structure and functionality of the imprinted pore is Studied through diffusion of the protein inside the pore immediately following polymerization. The imprinting effect is evaluated by comparing the interaction energy of the protein in the imprinted gel with the energy of a random process.