Gold and silver display a very wide range of optical and biological properties that make them applicable to many fields of science, engineering and medicine. Techniques such as Surface Enhanced Raman Spectroscopy (SERS) utilize size and shape optimized silver and gold nanoparticle substrates to enhance scattering intensity via surface plasmon effects. With this enhancement researchers have been able to probe single molecules. There is potential for controlling the size, shape and spacing of these nanoparticles through interactions with macromolecules. Other possible applications for these specialized nanoparticles include the development of smart materials and surface functionalization. To maximize outcomes in this area, an in depth atomistic level understanding of how macromolecules interact with these nanoparticles will be required. In biological and bio-medical sciences, gold and silver nanoparticles have already shown great potential for diagnostic and therapeutic applications. Molecular modeling can help us understand at a nanoscale level the unique biological responses to these metals which may in turn help drug designers better target diseases such as prostate cancer and Alzheimer’s disease.