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 uses simulation based approaches, and related statistical mechanics, classical and quantum mechanical methods, as a complementary tool to experiments.
Recent Publications
Xin Y., Gadda G., Hamelberg D., (2009). Cluster of Hydrophobic Residues Controls the Entrance to the Active Site of Choline Oxidase Biochemistry, 48, 9599-9605
Knight J. D. R., Hamelberg D., McCammon J. A., Kothary R., (2009). The role conserved water molecules in the catalytic domian of protein kinases Proteins: Structure, Function, and Bioinformatics, 76, 527-535
Hamelberg D., McCammon J. A., (2009). Mechanistic Insight into the Role of Transition-State Stabilization in Cyclophilin A. Journal of the American Chemical Society, 131, 147-152
Shen T., Hamelberg D., (2008). A statistical analysis of the precision of reweighting-based simulations. Journal of Chemical Physics, 129, 034103
Fajer M., Hamelberg D., McCammon J. A., (2008). Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. Journal of Chemical Theory and Computation, 4, 1565-1569
Qvist J., Davidovic M., Hamelberg D., Halle B., (2008). A dry ligand-binding cavity in a solvated protein. Proceedings of the National Academy of Sciences of the United States of America, 105, 6296-6301