Proteins are an integral aspect of biological systems, controlling the processes that mediate chemical balances within the organisms as well as serving as structural materials. The field of protein research however is vast with multiple levels of detail available to study. Computational modeling of proteins on an individual basis can allow us to study the dynamics of folding and location of secondary structure within sequences. In contrast, the study of larger systems containing multiple proteins can be used to understand how protein come together to form higher level structures. The qualitative molecular level insight that computational techniques can provide about the specific intra- and inter- protein interactions that underlie protein structure and function will guide the development of new peptides and macromolecules that can be specialized and optimized for different tasks in both biological systems as well as in composite materials.