Nanoscale particles have become promising materials in various biomedical applications, however, in order to stimulate and facilitate these applications, there is an urgent need for a better understanding of their biological effects as well. In this talk, I will discuss some of our recent molecular modeling work on nanotoxicity and their implications in de novo design of nanomedicine with IBM Blue Gene supercomputer. We show that carbon-based nanoparticles (carbon nanotubes, graphene nanosheets, and fullerenes) can interact and disrupt the structures and functions of many important proteins, such as WW domain involved in protein-protein interactions (PpI) and CYP3A4 enzyme.