2024
An Evaluation of Force Field Accuracy for the Mini-Protein Chignolin using Markov State Models. Tim Marshall, Robert M Raddi, Vincent A. Voelz. ChemRxiv. 2024; https://doi.org/10.26434/chemrxiv-2024-xmztm
Improved Estimates of Folding Stabilities and Kinetics with Multiensemble Markov Models. Si Zhang, Yunhui Ge, and Vincent A. Voelz. ChemRxiv. 2024; https://doi.org/10.26434/chemrxiv-2024-3wdwv
Automated optimization of force field parameters against ensemble-averaged measurements with Bayesian Inference of Conformational Populations. Robert M. Raddi and Vincent A. Voelz. arXiv: https://arxiv.org/abs/2402.11169
2023
A Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide Binding. Robert M. Raddi and Vincent A. Voelz. J. Phys. Chem. B. 2023, 127 (50): 10682–10690. DOI: https://doi.org/10.1021/acs.jpcb.3c04775
Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host–guest challenge. Matthew F. D. Hurley*, Robert M. Raddi*, Jason G. Pattis and Vincent A. Voelz. (*contributed equally) Phys. Chem. Chem. Phys., 2023, 25: 32393-32406. DOI: 10.1039/D3CP02197A.
Open Science Discovery of Potent Noncovalent SARS-CoV-2 Main Protease Inhibitors. Boby, Melissa L., Daren Fearon, Matteo Ferla, Mihajlo Filep, Lizbé Koekemoer, Matthew C. Robinson, The COVID Moonshot Consortium, et al. Science 382, no. 6671 (November 10, 2023): eabo7201. https://doi.org/10.1126/science.abo7201
Drug Discovery in Low Data Regimes: Leveraging a Computational Pipeline for the Discovery of Novel SARS-CoV-2 Nsp14-MTase Inhibitors. AkshatKumar Nigam, Matthew F. D. Hurley, Fengling Li, Eva Konkoĺová, Martin Klíma, Jana Trylčová, Robert Pollice, Süleyman Selim Çınaroğlu, Roni Levin-Konigsberg, Jasemine Handjaya, Matthieu Schapira, Irene Chau, Sumera Perveen, Ho-Leung Ng, H. Ümit Kaniskan, Yulin Han, Sukrit Singh, Christoph Gorgulla, Anshul Kundaje, Jian Jin, Vincent A Voelz, Jan Weber, Radim Nencka, Evzen Boura, Masoud Vedadi, Alán Aspuru-Guzik. bioRxiv 2023.10.03.560722; doi: https://doi.org/10.1101/2023.10.03.560722
Model selection using replica averaging with Bayesian inference of conformational populations. Raddi RM, Marshall T, Ge Y, Voelz V. ChemRxiv: https://doi.org/10.26434/chemrxiv-2023-396mm
BICePs v2.0: Software for Ensemble Reweighting using Bayesian Inference of Conformational Populations. Robert M. Raddi, Yunhui Ge and Vincent A. Voelz. J. Chem. Inf. Model. 2023, 63, 2370−2381: https://doi.org/10.1021/acs.jcim.2c01296
Folding@home: achievements from over twenty years of citizen science herald the exascale era. Vincent A. Voelz, Vijay S. Pande, and Gregory R. Bowman. Biophys. J. 2023, 122 (14): P2852-2863. https://doi.org/10.1016/j.bpj.2023.03.028
Structure-Based Experimental Datasets for Benchmarking of Protein Simulation Force Fields
Cavender, Chapin E.; Case, David A.; Chen, Julian C.-H.; Chong, Lillian T.; Keedy, Daniel A.; Lindorff-Larsen, Kresten; Mobley, David L.; Ollila, O.H. Samuli; Oostenbrink, Chris; Robustelli, Paul; Voelz, Vincent A.; Wall, Michael E.; Wych, David C.; Gilson, Michael K. Preprint: https://doi.org/10.5281/zenodo.7697462
2022
Effects of salinity and temperature on the flexibility and function of a polyextremophilic enzyme. Victoria J. Laye, Shahlo Solieva, Vincent A. Voelz and Shiladitya DasSarma. Int. J. Mol. Sci. 2022, 23(24), 15620; https://doi.org/10.3390/ijms232415620
Oncogenic mutations in the DNA-binding domain of FOXO1 disrupt folding: quantitative insights from experiments and molecular simulations. Dylan Novack, Lei Qian, Gwyneth Acker, Vincent A. Voelz, Richard H. G. Baxter. Biochemistry 2022, 61 (16): 1669–1682. https://doi.org/10.1021/acs.biochem.2c00224.
Estimation of binding rates and affinities from multiensemble Markov models and ligand decoupling. Ge, Yunhui, and Vincent A. Voelz. The Journal of Chemical Physics 156, no. 13 (April 7, 2022): 134115. https://doi.org/10.1063/5.0088024.
Unprotected Peptide Macrocyclization and Stapling via A Fluorine-Thiol Displacement Reaction. Md Shafiqul Islam, Samuel Junod, Si Zhang, Zakey Buuh, Yifu Guan, Mi Zhao, Kishan Kaneria, Parmila Kafley, Carson Cohen, Robert Maloney, Zhigang Lyu, Vincent A. Voelz, Weidong Yang, and Rongsheng Wang. Nature Communications 13, 350 (2022). https://doi.org/10.1038/s41467-022-27995-5
2021
Expanded ensemble methods can be used to accurately predict protein-ligand relative binding free energies. Si Zhang, David F. Hahn, Michael R. Shirts and Vincent A. Voelz. Journal of Chemical Theory and Computation, 17 (10): 6536–47 (2021) https://doi.org/10.1021/acs.jctc.1c00513
Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge. Robert M. Raddi and Vincent A. Voelz. Journal of Computer-Aided Molecular Design 35:953–961 (2021) https://doi.org/10.1007/s10822-021-00411-8
Assigning Confidence to Molecular Property Prediction. AkshatKumar Nigam, Robert Pollice, Matthew F. D. Hurley, Riley J. Hickman, Matteo Aldeghi, Naruki Yoshikawa, Seyone Chithrananda, Vincent A. Voelz, and Alán Aspuru-Guzik. Expert Opinion On Drug Discovery (2021). https://doi.org/10.1080/17460441.2021.1925247
Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution. Matthew F. D. Hurley, Justin D. Northrup, Yunhui Ge, Christian E. Schafmeister, Vincent A. Voelz. (2021) Journal of Chemical Information and Modeling, 61(6): 2818–2828 https://doi.org/10.1021/acs.jcim.1c00447
SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome. Maxwell I. Zimmerman, Justin R. Porter, Michael D. Ward, Sukrit Singh, Neha Vithani, Artur Meller, Upasana L. Mallimadugula, Catherine E. Kuhn, Jonathan H. Borowsky, Rafal P. Wiewiora, Matthew F. D. Hurley, Aoife M. Harbison, Carl A. Fogarty, Joseph E. Coffland, Elisa Fadda, Vincent A. Voelz, John D. Chodera, Gregory R. Bowman. Nature Chemistry 13: 651–659 (2021) https://doi.org/10.1038/s41557-021-00707-0
Solution-state preorganization of cyclic β-hairpin ligands determines binding mechanism and affinities for MDM2. Yunhui Ge, Si Zhang, Mate Erdelyi, and Vincent A. Voelz. Journal of Chemical Information and Modeling (2021) 61 (5): 2353–2367. https://doi.org/10.1021/acs.jcim.1c00029
Reconciling simulations and experiments with BICePs: a review. Vincent A. Voelz, Yunhui Ge and Robert M. Raddi. Frontiers in Molecular Biosciences: Biological Modeling and Simulation 8:325 (2021) https://doi.org/10.3389/fmolb.2021.661520
Metal-Binding Q-Proline Macrocycles. Justin D. Northrup, Jesse Wiener, Matthew F. D. Hurley, Chun-Feng David Hou, Taylor Keller, Richard Baxter, Michael J. Zdilla, Vincent A. Voelz, Christian E. Schafmeister. (2021). Journal of Organic Chemistry 86 (6): 4867–76. https://doi.org/10.1021/acs.joc.1c00116
Markov State Models to Elucidate Ligand Binding Mechanism. Ge Y., Voelz V.A. (2021) . In: Ballante F. (eds) Protein-Ligand Interactions and Drug Design. Methods in Molecular Biology, vol 2266. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1209-5_14
2020
Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning. The COVID Moonshot Consortium (130+ authors): Achdout, H., Aimon, A., Bar-David, E., et al. BioRxiv https://www.biorxiv.org/content/10.1101/2020.10.29.339317v1
Microcanonical coarse-graining of the kinetic Ising model. Daniel Sigg, Vincent Voelz, and Vincenzo Carnevale. Journal of Chemical Physics 152(8):084104 (2020 ). doi: 10.1063/1.5139228.
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). doi:10.1021/acs.jctc.9b01240.
Adaptive Markov State Model estimation using short reseeding trajectories. Hongbin Wan, Vincent A. Voelz. Journal of Chemical Physics 152, 024103 (2020) doi:10.1063/1.5142457
2019
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
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) doi:10.1021/acs.jpcb.7b11871
Elucidating the inhibition of peptidoglycan biosynthesis in Staphylococcus aureus by albocycline, a macrolactone isolated from Streptomyces maizeus. Liang, 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