Research in Biomolecular Simulations Group (Moradi Lab) is centered around two inter-related questions: (i) how do proteins function by changing their conformation and undergoing concerted motions? and (ii) how can we simulate these functionally important conformational changes at an atomic level?
We develop and employ Molecular Dynamics (MD) based enhanced sampling techniques to tackle both problems. Answering these questions would shed light on the structure-function relationships in proteins, and could improve our understanding of disease at a molecular level. We attempt to narrow the gap between the state-of-the-art computational methodologies and biologically/biomedically relevant applications.
We are particularly interested in the study of large-scale conformational changes of proteins such as those involved in membrane transport and signal transduction. A novel combination of nonequilibrium and equilibrium MD based techniques are employed to reconstruct the slow biomolecular processes such as inward- to outward-facing structural transition of membrane transporters at an atomic level.