B.S. (1999) University of Minnesota
Ph.D (2007) University of California - San Francisco
Beury Hall 130
The research in my group focuses on using transferrable, all-atom simulations for prediction and design of biomolecular dynamics and function. Recently, Markov State Model (MSM) approaches have been successful in constructing kinetic network models of protein folding from large-scale simulation data. MSMs are a new multiscale sample paradigm in which long timescale dynamics can be obtained from much shorter trajectories that sample transitions between metastable conformational states. We would like to extend these approaches to folding and design applications, where sampling both conformational and sequence space is imperative. Our interests include in silico prediction and design of proteins, peptide mimetics (e.g. peptoids), and binding sequences for cell signaling peptides.
Glenn L. Butterfoss, Barney Yoo, Jonathan N. Jaworskic, Ilya Chorny, Ken A. Dill, Ronald N. Zuckermann, Richard Bonneau, Kent Kirshenbaum and Vincent A. Voelz. "De novo structure prediction and experimental characterization of folded peptoid oligomers." PNAS 109 (36): 14320-14325 (2012)
Vincent A Voelz, Marcus Jager, Shuhuai Yao, Yujie Chen, Li Zhu, Steven A. Waldauer, Gregory R. Bowman, Mark Friedrichs, Olgica Bakajin, Lisa J. Lapidus, Shimon Weiss, and Vijay S. Pande. "Slow unfolded-state structuring in ACBP folding revealed by simulation and experiment. " JACS 134 (30): 12565–12577 (2012).
Thomas J. Lane, Gregory R. Bowman, Kyle Beauchamp, Vincent A. Voelz and Vijay S. Pande. "Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories." JACS 133(45):18413–18419 (2011).
Bowman, G.R.; Voelz, V.A.; Pande, V.S. "Atomistic Folding Simulations of the Five-Helix Bundle Protein lambda(6-85)." J. Am. Chem. Soc. 133(4): 664-667 (2011).
Bowman, G.R.; Voelz, V.A.; Pande, V.S. "Taming the complexity of protein folding." Current Opinion in Structural Biology 1:4-11 (2011).
Voelz, V.A.; Dill, K.A.; Chorny, I. "Peptiod Conformational Free Energy landscapes From Implicit-Solvent Molecular Simulations in AMBER." Biopolymers 96(5):639-650 (2011).
Voelz, V.A.; Bowman, G.R.; Beauchamp, K.; Pande, V.S. "Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)." J. Am. Chem. Soc. 132(5): 1526-1528 (2010).
Voelz, V.A.; Singh, V.R.; Wedemeyer, W.J.; Lapidus, L.J.; Pande, V.S. "Unfolded state dynamics and structure of protein L characterized by simulation and experiment." J. Am. Chem. Soc. 132(13): 4702-4709 (2010).
Voelz, V.A.; Luttmann, E.; Bowman, G.R.; Pande, V.S. "Probing the nanosecond dynamics of a designed three-stranded beta-sheet with massicely parallel molecular dynamics simulation." International Journal of Molecular Sciences. 10(3): 1013-1030 (2009).
Shell, M.S.; Oxkan, S.B.; Voelz, V.; Wu, G.A.; Dill, K.A. "A Blind Test of Physics-Based Prediction of Protein Structure." Biophysical Journal. 96(3): 917-924 (2009).
Voelz, V.; Shell, M.S.; Dill, K.A. "Predicting peptide structures in native proteins from physical simulations." PLoS Computational Biology. 5(2): 1000281 (2009).