Publications

Adaptive Markov State Model estimation using short reseeding trajectories. Hongbin Wan, Vincent A. Voelz. Submitted (2019)

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. Submitted (2019). [bioRxiv]

A Site-Specific ImmunoPET Tracer to Image PD-L1. Haley L Wissler, Emily B Ehlerding, Zhigang Lyu, Yue Zhao, Si Zhang, Anisa Eshraghi, Zakey Yusuf Buuh, Jeffrey C McGuth, Yifu Guan, Jonathan W Engle, Sarah J Bartlett, Vincent A Voelz, Weibo Cai, Rongsheng E Wang. Molecular pharmaceutics. 16 (5), pp 2028–2036 (2019) doi:10.1021/acs.molpharmaceut.9b00010

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). doi:10.1021/acs.jpcb.8b12220

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). doi:10.1021/jacs.8b13498

2018

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). doi:10.1074/JBC.RA118.004909
* JBC Editors’ Pick, commentary article

Is the free energy landscape informative about transition rates? Lessons from the kinetic Ising model. Daniel Sigg, Vincent Voelz, and Vincenzo Carnevale, Submitted. [Arxiv preprint]

Model selection using BICePs: A Bayesian approach to force field validation and parameterizationYunhui Ge and Vincent A. Voelz, Journal of Physical Chemistry B 122 (21): 5610–5622 (2018) doi:10.1021/acs.jpcb.7b11871

Elucidating the inhibition of peptidoglycan biosynthesis in Staphylococcus aureus by albocycline, a macrolactone isolated from Streptomyces maizeusLiang, Hai; Zhou, Guangfeng; Ge, Yunhui; D’Ambrosio, Elizabeth; Eidem, Tess; Blanchard, Catlyn; Louka, Cindy; Chatare, Vijay; Dunman, Paul; Valentine, Ann; Voelz, Vincent; Grimes, Catherine; Andrade, Rodrigo, Bioorganic & Medicinal Chemistry 26(12): 3453-3460 (2018). doi:10.1016/j.bmc.2018.05.017


2017

Control of porphyrin interactions via structural change of peptoid scaffold. Woojin Yang, Boyeong Kang, Vincent A. Voelz, Jiwon Seo, Org. Biomol. Chem. 15: 9670-9679 (2017) doi:10.1039/C7OB02398G

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 113 (4): 785–793 (2017).   doi:10.1016/j.bpj.2017.07.009

Precisely tuneable energy transfer system using peptoid helix-based molecular scaffold.Boyeong Kang , Woojin Yang , Sebok Lee , Sudipto Mukherjee, Jonathan Forstater, Hanna Kim, Byoungsook Goh, Tae-Young Kim, Vincent Voelz, Yoonsoo Pang, Jiwon Seo.  Scientific Reports 7: 4786 (2017) doi:10.1038/s41598-017-04727-0 

Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models. Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. Journal of Chemical Information and Modeling 57 (7): 1609–1620 (2017). doi:10.1021/acs.jcim.7b00132

Molecular simulations and free-energy calculations suggest conformation-dependent anion binding to a cytoplasmic site as a mechanism for Na+/K+-ATPase ion selectivity. Asghar M. Razavi, Lucie Delemotte, Joshua R. Berlin, Vincenzo Carnevale, and Vincent A. Voelz. Journal of Biological Chemistry 292: 12412-12423 (2017). doi:10.1074/jbc.M117.779090

The Diverted Total Synthesis of Carolacton-Inspired Analogs Yields Three Distinct Phenotypes in Streptococcus mutans Biofilms. Amy E. Solinski, Alexander Koval, Richard Brzozowski, Kelly Morrison, Americo J. Fraboni, Carrie Carson, Anisa Eshraghi, Guangfeng Zhou, Robert Quivey, Vincent A. Voelz, Bettina A. Buttaro, and William M. Wuest. Journal of the American Chemical Society 139 (21): 7188–7191 (2017). doi:10.1021/jacs.7b03879

2016

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) doi:10.1021/acs.jctc.6b00938

Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking.  Sudipto Mukherjee, George A. Pantelopulos, and Vincent A. Voelz. Scientific Reports 6: 31631 (2016). doi:10.1038/srep31631

Using kinetic network models to probe non-native salt-bridge effects on α-helix folding. Guangfeng Zhou and Vincent A. Voelz. Journal of Physical Chemistry B 120(5):926–935 (2016). doi:10.1021/acs.jpcb.5b11767


2015

Insights into peptoid helix folding cooperativity from an improved backbone potential. Sudipto Mukherjee, Guangfeng Zhou, Chris Michel and Vincent A. Voelz. Journal of Physical Chemistry B 119 (50):15407–15417 (2015). doi:10.1021/acs.jpcb.5b09625

Microsecond simulations of MDM2 and its complex with p53 yield insight into force field accuracy and conformational dynamics
George A. Pantelopulos and Vincent A. Voelz. Proteins: Structure, Function and Bioinformatics 83 (9): 1665–1676 (2015). doi:10.1002/prot.24852

Kinetic network models of tryptophan mutations in β-hairpins reveal the importance of non-native interactions. Asghar M. Razavi and Vincent A. Voelz. Journal of Chemical Theory and Computation 11(6): 2801–2812 (2015). doi:10.1021/acs.jctc.5b00088

Molecular simulation of conformational pre-organization in cyclic RGD peptides
Amanda E. Wakefield, William M. Wuest, and Vincent A. Voelz. Journal of Chemical Information and Modeling 55 (4), pp 806–813 (2015).  doi:10.1021/ci500768u

2014

Surprisal metrics for quantifying perturbed conformational dynamics in Markov State Models. Vincent A Voelz, Brandon Elman, Asghar M Razavi, Guangfeng Zhou. Journal of Chemical Theory and Computation 10 (12):5716–5728 (2014)  doi:10.1021/ct500827g

Bayesian inference of conformational state populations from computational models and sparse experimental observables. Vincent A. Voelz and Guangfeng Zhou. Journal of Computational Chemistry 35(30):2215–2224 (2014). doi:10.1002/jcc.23738

Computational screening and selection of cyclic peptide hairpin mimetics by molecular simulation and kinetic network models. Asghar M. Razavi , William M. Wuest and Vincent A. Voelz. Journal of Chemical Information and Modeling 54(5): 1425–1432 (2014). doi:10.1021/ci500102y

A Molecular Interpretation of 2D IR Protein Folding Experiments with Markov State Models. Carlos R. Baiz, Yu-Shan Lin, Chunte Sam Peng, Kyle A. Beauchamp, Vincent A. Voelz, Vijay S. Pande and Andrei Tokmakoff. Biophysical Journal 106(6): 1359-1370 (2014). doi:10.1016/j.bpj.2014.02.008

2013

Probing Antibody Internal Dynamics with Fluorescence Anisotropy and Molecular Dynamics Simulations. Ekaterine Kortkhonjia, Relly Brandman, Joe Zhou, Vincent A. Voelz, Ilya Chorny, Ken A. Dill, Bruce Kabakoff, Tom Patapoff and Trevor E Swartz. MAbs 5(2) (2013) doi:10.4161/mabs.23651

2012

De novo structure prediction and experimental characterization of folded peptoid oligomers. Glenn L. Butterfoss, Barney Yoo, Jonathan N. Jaworskic, Ilya Chorny, Ken A. Dill, Ronald N. Zuckermann, Richard Bonneau, Kent Kirshenbaum and Vincent A. Voelz. Proceedings of the National Academy of Sciences 109 (36): 14320-14325 (2012). doi:10.1073/pnas.1209945109

Slow unfolded-state structuring in ACBP folding revealed by simulation and experiment. 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. Journal of the American Chemical Society 134 (30): 12565–12577 (2012). doi:10.1021/ja302528z

Calculation of Rate Spectra from Noisy Time Series Data. Vincent A. Voelz and Vijay S. Pande. Proteins: Structure, Function and Bioinformatics 80(2):335–675 (2012). doi:10.1002/prot.23171

2011

Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories. Thomas J. Lane, Gregory R. Bowman, Kyle Beauchamp, Vincent A. Voelz and Vijay S. Pande. Journal of the American Chemical Society 133(45):18413–18419 (2011). doi:10.1021/ja207470h

Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER. Vincent A. Voelz, Ken A. Dill and Ilya Chorny. Biopolymers 96(5): 639–650 (2011) doi:10.1002/bip.21575

Taming the complexity of protein folding. Gregory R. Bowman, Vincent A. Voelz and Vijay S. Pande. Current Opinion in Structural Biology 21(1):4-11 (2011) doi:10.1016/j.sbi.2010.10.006

Atomistic folding simulations of the five helix bundle protein λ6-85. Gregory R. Bowman, Vincent A. Voelz and Vijay S. Pande. Journal of the American Chemical Society 133(4): 664-667 (2011) doi:10.1021/ja106936n

2010

Unfolded state dynamics and structure of protein L characterized by simulation and experiment
Vincent A. Voelz, Vijay R. Singh, William J. Wedemeyer, Lisa J. Lapidus, Vijay S. Pande. Journal of the American Chemical Society, 132(13): 4702-4709 (2010) doi:10.1021/ja908369h

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). Vincent A. Voelz, Gregory R. Bowman, Kyle Beauchamp and Vijay S. Pande. Journal of the American Chemical Society, 132(5): 1526-1528 (2010) doi:10.1021/ja9090353  [movie]

2009

Probing the nanosecond dynamics of a designed three-stranded beta-sheet with massively parallel molecular dynamics simulation. Vincent A. Voelz, Edgar Luttmann, Gregory R. Bowman and Vijay S. Pande. International Journal of Molecular Sciences, 10(3): 1013-1030 (2009) doi:10.3390/ijms10031013

A Blind Test of Physics-Based Prediction of Protein Structures. M. Scott Shell, S. Banu Ozkan, Vincent Voelz, G. Albert Wu, and Ken A. Dill. Biophysical Journal, 96(3): 917-24 (2009) doi:10.1016/j.bpj.2008.11.009

Predicting peptide structures in native proteins from physical simulations. Vincent Voelz, M. Scott Shell and Ken A. Dill. PLoS Computational Biology, 5(2):e1000281 (2009) doi:10.1371/journal.pcbi.1000281

A multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnel. Vincent A. Voelz, Paula Petrone and Vijay S. Pande. Pacific Symposium on Biocomputing, 14:340-352 (2009). doi:10.1142/9789812836939_0032

2007 and earlier

The protein folding problem: when will it be solved? Dill KA, Ozkan SB, Weikl TR, Chodera JD, Voelz VA. Curr Opin Struct Biol, 17:342-346 (2007) doi:10.1016/j.sbi.2007.06.001

Exploring Zipping and Assembly as a Protein Folding Principle. Vincent A. Voelz and Ken A. Dill. Proteins: Structure, Function, and Bioinformatics, 66:877-888 (2007) doi:10.1002/prot.21234

Information Content of Molecular Structures. David C. Sullivan, Tiba Aynechi, Vincent A. Voelz, and Irwin D. Kuntz. Biophysical Journal 85(1): 174-190 (2003). doi:10.1016/S0006-3495(03)74464-6

Molecular dynamics simulation of site-directed spin labeling: experimental validation in muscle fibers. Leslie EW Laconte*, Vincent Voelz*, Wendy Nelson, and David. D. Thomas. Biophysical Journal. 83: 1854-1866 (2002). (*coauthors) doi:10.1016/S0006-3495(02)73950-7