The formation of magnetic bead or nanoparticle superstructures due to magnetic dipole dipole interactions can be used as configurable matter in order to realize low-cost magnetoresistive sensors with very high GMR-effect amplitudes. Experimentally, this can be realized by immersing magnetic beads or nanoparticles in conductive liquid gels and rearranging them by applying suitable external magnetic fields. After gelatinization of the gel matrix the bead or nanoparticle positions are fixed and the resulting system can be used as a magnetoresistive sensor. In order to optimize such sensor structures we have developed a simulation tool chain that allows us not only to study the structuring process in the liquid state but also to rigorously calculate the magnetoresistive characteristic curves for arbitrary nanoparticle arrangements. As an application, we discuss the role of magnetoresistive sensors in finding answers to molecular recognition.