个人简介

B.S. (1999) University of Minnesota Ph.D (2007) University of California - San Francisco

研究领域

Biological Chemistry; Physical Chemistry

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.

近期论文

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Vincent A Voelz, Brandon Elman, Asghar M Razavi, Guangfeng Zhou."Surprisal metrics for quantifying perturbed conformational dynamics in Markov State Models" Journal of Chemical Theory and Computation, 10 (12):5716–5728 (2014) Vincent A. Voelz and Guangfeng Zhou. "Bayesian inference of conformational state populations from computational models and sparse experimental observables" Journal of Computational Chemistry, 35(30):2215–2224 (2014) Asghar M. Razavi , William M. Wuest and Vincent A. Voelz "Computational screening and selection of cyclic peptide hairpin mimetics by molecular simulation and kinetic network models" Journal of Chemical Information and Modeling, 54(5): 1425–1432 (2014) Carlos R. Baiz, Yu-Shan Lin, Chunte Sam Peng, Kyle A. Beauchamp, Vincent A. Voelz, Vijay S. Pande and Andrei Tokmakoff. "A Molecular Interpretation of 2D IR Protein Folding Experiments with Markov State Models" Biophysical Journal 106(6): 1359-1370 (2014) Ekaterine Kortkhonjia, Relly Brandman, Joe Zhou, Vincent A. Voelz, Ilya Chorny, Ken A. Dill, Bruce Kabakoff, Tom Patapoff and Trevor E Swartz."Probing Antibody Internal Dynamics with Fluorescence Anisotropy and Molecular Dynamics Simulations" MAbs 5(2) (2013) 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) Vincent A. Voelz and Vijay S. Pande. "Calculation of Rate Spectra from Noisy Time Series Data" Proteins: Structure, Function and Bioinformatics 80(2):335–675 (2012) 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).