The overall goal of this project is to understand how protein structures have evolved. We want to understand how much of the sequence diversity observed in current proteins can be explained by thermodynamic constraints on protein stability. We also want to understand how co-evolution between different sites in a protein emerges and different mechanisms behind a central property in evolutionary biology - epistasis/
We develop method to simulate the evolution of protein sequences by combining the theory of evolutionary dynamics and structure-based energy calculations. We develop our simulation tools based on the ROSETTA macromolecular modeling suite. ROSETTA is the leading program package for both structure prediction and protein design.