Using molecular dynamics simulations, X-ray crystallography and a range of biophysical techniques, we try to understand the role of conformational change and flexibility in protein function. We approach this from two directions: first using simulation and bioinformatics to provide experimentally testable predictions, and second to provide a theoretical framework for interpreting existing experimental data. We study a broad range of systems, including the dynamics of pMHC-TCR interactions, serpin misfolding and disease, PolyQ-mediated aggregation, disorder in disease-causing mutations, and the structural basis for autoantibody-antigen engagement.