The research in our group focuses on the application and development of theoretical and computational methods with the intent of gaining an in-depth understanding of biomolecular switches. Many interactions in cell signaling pathways are mediated by intricate networks of interacting proteins and RNAs. Deregulation of these pathways could trigger cellular transformation, oncogenesis, and a host of other diseases. The research in our lab seeks to decipher the underlying principles governing cell signaling mechanisms and biomolecular interactions involving proteins and RNAs. In these endeavors, we use simulation based approaches, and related statistical mechanics, classical and quantum mechanical methods, as a complementary tool to experiments.
Recent Selected Publications
Doshi U., Holliday M. J., Eisenmesser E. Z., Hamelberg D., (2016). Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation. Proceedings of the National Academy of Sciences of the United States of America, 113, 4735–4740
Barman A., Hamelberg D., (2016). Coupled Dynamics and Entropic Contribution to the Allosteric Mechanism of Pin1. Journal of Physical Chemistry B, 120, 8405−8415
Barman A., Smitherman C., Souffrant M., Gadda G., Hamelberg D., (2016). Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins. Journal of Chemical Information and Modeling, 56, 139-147
Ho K. C., Hamelberg D., (2016). Oscillatory Diffusion and Second-Order Cyclostationarity in Alanine Tripeptide from Molecular Dynamics Simulation. Journal of Chemical Theory and Computation, 12, 372–382
Rodriguez-Bussey I. G., Doshi U., Hamelberg D., (2016). Enhanced molecular dynamics sampling of drug target conformations. Biopolymers, 105, 35-42
Tork-Ladani S., Souffrant M. G.,Barman A., Hamelberg D., (2015). Computational perspective and evaluation of plausible catalytic mechanisms of peptidyl-prolyl cis-trans isomerases. Biochimica et Biophysica ACTA-General Subjects, 1850, 1994-2004