The Voelz group uses biomolecular simulation and statistical mechanics to study protein folding, ligand binding, and molecular design. From large numbers of simulation trajectories generated on distributed computing platforms, we construct Markov state models (MSMs) of conformational dynamics, which can be used to efficiently estimate mechanistic information about pathways and rates. Through these methods and others, we aim to predict and design properties of cyclic peptides and other peptidomimetics. We also develop Bayesian inference approaches to model structural ensembles using a combination of experiment and theory.
Reconciling simulated ensembles of apomyoglobin with experimental HDX data using Bayesian inference and multi-ensemble Markov State Models. Hongbin Wan, Yunhui Ge, Asghar Razavi, Vincent A Voelz. Journal of Chemical Theory and Computation 16(2): 1333-1348 (2020).
Adaptive Markov State Model estimation using short reseeding trajectories. Hongbin Wan, Vincent A. Voelz. Journal of Chemical Physics 152, 024103 (2020).
Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study. A Acharyya, Y Ge, H Wu, WF DeGrado, VA Voelz, F Gai. The Journal of Physical Chemistry B 123 (8), pp 1797–1807 (2019).
Fluorinated Aromatic Monomers as Building Blocks to Control α-Peptoid Conformation and Structure. Diana Gimenez, Guangfeng Zhou, Juan A. Aguilar, Vincent Voelz, and Steven L. Cobb. Journal of the American Chemical Society 141 (8), pp 3430–3434 (2019).
Simulations of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.* Yunhui Ge, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. Journal of Biological Chemistry 293 (51): 19532-19543 (2018).
* JBC Editors’ Pick, commentary article
Model selection using BICePs: A Bayesian approach to force field validation and parameterization. Yunhui Ge and Vincent A. Voelz, Journal of Physical Chemistry B 122 (21): 5610–5622 (2018).
Bridging microscopic and macroscopic mechanisms of p53-MDM2 binding using kinetic network models. Guangfeng Zhou, George A. Pantelopulos, Sudipto Mukherjee, and Vincent A. Voelz. Biophysical Journal (2017) 113 (4): 785–793.
A maximum-caliber approach to predicting perturbed folding kinetics due to mutations. Hongbin Wan, Guangfeng Zhou, and Vincent A. Voelz. Journal of Chemical Theory and Computation 12 (12): 5768–5776 (2016).