The function and interaction of proteins critically depends on their dynamics. Computer simulations provide a way to watch biomolecules in action and how they respond to external forces or chemical modifications. Molecular dynamics (MD) simulations in particular capture the behavior of biomolecules in full atomic detail and with high temporal resolution by solving Newton’s equations of motion for the whole atomic system. The availability of more powerful computer hardware and of an increased number of biomolecular structures have increased the impact of MD simulations in molecular biology and drug discovery.
In the Meiler lab, we apply MD simulations to study the interaction of drug molecules with pharmacologically important proteins such as protein kinases and membrane proteins. In addition, MD simulations methods with enhanced conformational sampling are used to investigate the impact of genetic variations on the 3-dimensional structure and dynamics of these proteins.
 Hanker, A. B., Brown, B. P., Meiler, J., Marín, A., Jayanthan, H. S., Ye, D., Lin, C.-C., Akamatsu, H., Lee, K.-M., Chatterjee, S., Sudhan, D. R., Servetto, A., Brewer, M. R., Koch, J. P., Sheehan, J. H., He, J., Lalani, A. S., & Arteaga, C. L. (2021). Co-occurring gain-of-function mutations in HER2 and HER3 modulate her2/her3 activation, oncogenesis, and HER2 inhibitor sensitivity. Cancer Cell, 39(8). https://doi.org/10.1016/j.ccell.2021.06.001
 Gulsevin A, Meiler J (2021) Prediction of amphipathic helix—membrane interactions with Rosetta. PLoS Comput Biol 17(3): e1008818. https://doi.org/10.1371/journal.pcbi.1008818