Defects strongly influence the electronic properties of graphene. It is of importance to get a deeper insight into the influence that defects have on electron transport. In this work we accurately model defect structures with density functional theory. We obtain tight-binding parameters via transforming the results into the basis of maximally localized Wannier orbitals. We can then treat large-scale structures with defects using a highly efficient tight-binding approach. To combine the defect structure calculations with the surrounding lattice, we present a new embedding technique that is applicable to a wide range of zero-dimensional defects. This technique defines a transition region between the tight-binding parameters of the bulk lattice and those obtained for the defect structure. To test our technique we model an experimental setup currently investigated at the University of Vienna. Our approach turns out to be applicable to a broad range of defects. Calculations were conducted for Stone-Wales defects, flower defects, double vacancies and silicon substitutes. The scattering at these defects could be investigated in detail for a wide range of energies. We find robust backscattering signatures of the defect symmetries that can be explained by the band structure of graphene.