The mechanism of specific adsorption of bio-macromolecules onto metallic and oxidic nanostructures will be explained in atomic resolution resulting from simulations with novel force fields and surface models in comparison to measurements. As an example, variations in peptide adsorption on Pd and Pt nanoparticles depending on shape, size, and location of peptides on specific bounding facets are determined by soft epitaxial processes and induced charges. On oxidic nanoparticles such as silica and apatites, it is shown how changes in pH lead to similarity scores of attracted peptides lower than 20%, supported by model surfaces of appropriate surface chemistry and adsorption isotherms. The results demonstrate how new computational methods can support the design of structured hydrogels, nanoparticle carriers for drug release, and the understanding of calcification mechanisms in the human body. The main features of the INTERFACE force field for accurate simulations of inorganic/organic and inorganic/biological interfaces will be discussed.