Theses and Dissertations Collection

Proteins are the molecular machines that perform the functions necessary for life. Interactions between proteins and other biomolecules are at the heart of all biological processes in a cell. This thesis explores how molecular modeling can be used to understand both proteins and their interactions. Examples include antibody-antigen interactions in Ebola, how proteins might behave in the subsurface oceans of Titan, and the ability of different software to accurately predict protein interactions. We predict mutations in Ebola that could lead to antibody escape. We explore aspects of possible life on exoplanets by modeling how Earth-based proteins would behave in the environment thought to exist in subsurface oceans on Titan. We analyze a suite of different software to find those that have better predictive capabilities, depending on the location and type of mutation. In short, we show that molecular modeling can be used to make predictions about protein behavior and interactions.