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Vincent A. Voelz - Publications

Affiliations: 
2011- Chemistry Temple University, Philadelphia, PA, United States 
Area:
molecular simulation of proteins and peptidomimetics
Website:
http://voelzlab.org
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74 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Raddi RM, Voelz VA. Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide Binding. The Journal of Physical Chemistry. B. PMID 38078851 DOI: 10.1021/acs.jpcb.3c04775  0.763
2023 Hurley MFD, Raddi RM, Pattis JG, Voelz VA. Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host-guest challenge. Physical Chemistry Chemical Physics : Pccp. PMID 38009066 DOI: 10.1039/d3cp02197a  0.767
2023 Boby ML, Fearon D, Ferla M, Filep M, Koekemoer L, Robinson MC, Chodera JD, Lee AA, London N, von Delft A, von Delft F, Achdout H, Aimon A, Alonzi DS, Arbon R, ... ... Voelz V, et al. Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors. Science (New York, N.Y.). 382: eabo7201. PMID 37943932 DOI: 10.1126/science.abo7201  0.674
2023 Raddi RM, Ge Y, Voelz VA. BICePs v2.0: Software for Ensemble Reweighting Using Bayesian Inference of Conformational Populations. Journal of Chemical Information and Modeling. PMID 37027181 DOI: 10.1021/acs.jcim.2c01296  0.756
2023 Voelz VA, Pande VS, Bowman GR. Folding@home: achievements from over twenty years of citizen science herald the exascale era. Arxiv. PMID 36994157  0.698
2023 Voelz VA, Pande VS, Bowman GR. Folding@home: Achievements from over 20 years of citizen science herald the exascale era. Biophysical Journal. PMID 36945779 DOI: 10.1016/j.bpj.2023.03.028  0.697
2022 Ge Y, Voelz VA. Estimation of binding rates and affinities from multiensemble Markov models and ligand decoupling. The Journal of Chemical Physics. 156: 134115. PMID 35395889 DOI: 10.1063/5.0088024  0.521
2021 Zhang S, Hahn DF, Shirts MR, Voelz VA. Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies. Journal of Chemical Theory and Computation. PMID 34516130 DOI: 10.1021/acs.jctc.1c00513  0.624
2021 Raddi RM, Voelz VA. Stacking Gaussian processes to improve [Formula: see text] predictions in the SAMPL7 challenge. Journal of Computer-Aided Molecular Design. PMID 34363562 DOI: 10.1007/s10822-021-00411-8  0.747
2021 Hurley MFD, Northrup JD, Ge Y, Schafmeister CE, Voelz VA. Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution. Journal of Chemical Information and Modeling. PMID 34125519 DOI: 10.1021/acs.jcim.1c00447  0.546
2021 Voelz VA, Ge Y, Raddi RM. Reconciling Simulations and Experiments With BICePs: A Review. Frontiers in Molecular Biosciences. 8: 661520. PMID 34046431 DOI: 10.3389/fmolb.2021.661520  0.754
2021 Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, ... Voelz VA, et al. SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome. Nature Chemistry. PMID 34031561 DOI: 10.1038/s41557-021-00707-0  0.743
2021 Ge Y, Zhang S, Erdelyi M, Voelz VA. Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2. Journal of Chemical Information and Modeling. PMID 33905247 DOI: 10.1021/acs.jcim.1c00029  0.558
2021 Ge Y, Voelz VA. Markov State Models to Elucidate Ligand Binding Mechanism. Methods in Molecular Biology (Clifton, N.J.). 2266: 239-259. PMID 33759131 DOI: 10.1007/978-1-0716-1209-5_14  0.539
2020 Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, ... Voelz VA, et al. Citizen Scientists Create an Exascale Computer to Combat COVID-19. Biorxiv : the Preprint Server For Biology. PMID 32637963 DOI: 10.1101/2020.06.27.175430  0.728
2020 Sigg D, Voelz VA, Carnevale V. Microcanonical coarse-graining of the kinetic Ising model. The Journal of Chemical Physics. 152: 084104. PMID 32113343 DOI: 10.1063/1.5139228  0.346
2020 Wan H, Voelz VA. Adaptive Markov state model estimation using short reseeding trajectories. The Journal of Chemical Physics. 152: 024103. PMID 31941308 DOI: 10.1063/1.5142457  0.445
2020 Wan H, Ge Y, Razavi A, Voelz VA. Reconciling simulated ensembles of apomyoglobin with experimental HDX data using Bayesian inference and multi-ensemble Markov State Models. Journal of Chemical Theory and Computation. PMID 31917926 DOI: 10.1021/Acs.Jctc.9B01240  0.636
2020 Ge Y, Voelz VA. Efficient Estimation of Binding Kinetics using Scaled Non-Bonded Interactions and Harmonic Restraints Biophysical Journal. 118: 140a. DOI: 10.1016/J.Bpj.2019.11.890  0.493
2020 Ge Y, Raddi RM, Voelz VA. BICePs 2.0: New Tools for Bayesian Inference of Conformational Populations from Theory and Experiment Biophysical Journal. 118: 139a-140a. DOI: 10.1016/J.Bpj.2019.11.888  0.504
2020 Zhang S, Voelz V. Improved Estimates of Folding Stabilities and Kinetics from Multiensemble Markov Models Biophysical Journal. 118: 139a. DOI: 10.1016/J.Bpj.2019.11.884  0.315
2020 Solieva S, Voelz VA. Using Molecular Simulation to Understand the Role of Conserved Residues in an Extremophilic Beta-Galactosidase Biophysical Journal. 118: 506a. DOI: 10.1016/J.Bpj.2019.11.2789  0.332
2020 Hurley MF, Voelz V. Binding of MDM2 Inhibitors via Biased Sampling and Multi-Ensemble Markov Models Biophysical Journal. 118: 298a-299a. DOI: 10.1016/J.Bpj.2019.11.1691  0.329
2020 Voelz VA. Unveiling Ligand Binding Mechanisms through Molecular Simulation: Lessons and Progress from Markov State Model Approaches Biophysical Journal. 118: 179a-180a. DOI: 10.1016/J.Bpj.2019.11.1097  0.409
2019 Acharyya A, Ge Y, Wu H, DeGrado WF, Voelz VA, Gai F. Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study. The Journal of Physical Chemistry. B. PMID 30694671 DOI: 10.1021/Acs.Jpcb.8B12220  0.566
2019 Acharyya A, Ge Y, Wu H, DeGrado W, Voelz V, Gai F. Exposing the Nucleation Site of Alpha Helix Folding: A Joint Experimental and Simulation Study Biophysical Journal. 116: 310a. DOI: 10.1016/J.Bpj.2018.11.1679  0.514
2019 Wan H, Voelz V. On the Use of Short Reseeding Trajectories to Sample Markov State Models Biophysical Journal. 116: 289a. DOI: 10.1016/J.Bpj.2018.11.1562  0.322
2019 Ge Y, Voelz V. Using Computational Modeling to Understand the Binding Mechanism of Designed Cyclic β-Hairpin to MDM2 Biophysical Journal. 116: 193a. DOI: 10.1016/J.Bpj.2018.11.1068  0.511
2018 Ge Y, Borne E, Stewart S, Hansen MR, Arturo EC, Jaffe EK, Voelz VA. Simulations of the regulatory ACT domain of human phenylalanine hydroxylase unveil its mechanism of phenylalanine binding. The Journal of Biological Chemistry. PMID 30287685 DOI: 10.1074/Jbc.Ra118.004909  0.604
2018 Liang H, Zhou G, Ge Y, D'Ambrosio EA, Eidem TM, Blanchard C, Shehatou C, Chatare VK, Dunman PM, Valentine AM, Voelz VA, Grimes CL, Andrade RB. Elucidating the inhibition of peptidoglycan biosynthesis in Staphylococcus aureus by albocycline, a macrolactone isolated from Streptomyces maizeus. Bioorganic & Medicinal Chemistry. PMID 29805074 DOI: 10.1016/J.Bmc.2018.05.017  0.479
2018 Ge Y, Voelz VA. Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and Parameterization. The Journal of Physical Chemistry. B. PMID 29518328 DOI: 10.1021/Acs.Jpcb.7B11871  0.6
2018 Wan H, Ge Y, Razavi A, Voelz V. Reconciling Simulated Ensembles of Apomyoglobin with Experimental HDX Data Biophysical Journal. 114: 680a-681a. DOI: 10.1016/J.Bpj.2017.11.3671  0.547
2018 Hurley M, Northrup J, Voelz V, Schafmeister C. Enhanced Sampling and Bayesian Inference to Model the Conformational Dynamics of Peptoid Macrocycles Biophysical Journal. 114: 558a. DOI: 10.1016/J.Bpj.2017.11.3049  0.36
2018 Ge Y, Jaffe EK, Voelz VA. Binding Pathways of Phenylalanine to the Dimeric Regulatory Domain of Human PAH Reveal a LID Gating Mechanism Biophysical Journal. 114: 226a. DOI: 10.1016/J.Bpj.2017.11.1257  0.481
2017 Yang W, Kang B, Voelz VA, Seo J. Control of porphyrin interactions via structural changes of a peptoid scaffold. Organic & Biomolecular Chemistry. PMID 29119173 DOI: 10.1039/C7Ob02398G  0.31
2017 Zhou G, Pantelopulos GA, Mukherjee S, Voelz VA. Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network Models. Biophysical Journal. 113: 785-793. PMID 28834715 DOI: 10.1016/J.Bpj.2017.07.009  0.423
2017 Ge Y, Kier BL, Andersen NH, Voelz VA. Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models. Journal of Chemical Information and Modeling. PMID 28614661 DOI: 10.1021/Acs.Jcim.7B00132  0.63
2017 Razavi AM, Delemotte L, Berlin JR, Carnevale V, Voelz VA. Molecular simulations and free-energy calculations suggest conformation-dependent anion binding to a cytoplasmic site as a mechanism for Na(+)/K(+)-ATPase ion selectivity. The Journal of Biological Chemistry. PMID 28588025 DOI: 10.1074/Jbc.M117.779090  0.365
2016 Wan H, Zhou G, Voelz VA. A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations. Journal of Chemical Theory and Computation. 12: 5768-5776. PMID 27951664 DOI: 10.1021/Acs.Jctc.6B00938  0.435
2016 Mukherjee S, Pantelopulos GA, Voelz VA. Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking. Scientific Reports. 6: 31631. PMID 27538695 DOI: 10.1038/Srep31631  0.393
2016 Zhou G, Voelz VA. Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding. The Journal of Physical Chemistry. B. PMID 26769494 DOI: 10.1021/Acs.Jpcb.5B11767  0.466
2015 Mukherjee S, Zhou G, Michel C, Voelz VA. Insights Into Peptoid Helix Folding Cooperativity From an Improved Backbone Potential. The Journal of Physical Chemistry. B. PMID 26584227 DOI: 10.1021/Acs.Jpcb.5B09625  0.482
2015 Razavi AM, Voelz VA. Kinetic Network Models of Tryptophan Mutations in β-Hairpins Reveal the Importance of Non-Native Interactions. Journal of Chemical Theory and Computation. 11: 2801-12. PMID 26575573 DOI: 10.1021/Acs.Jctc.5B00088  0.422
2015 Pantelopulos GA, Mukherjee S, Voelz VA. Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics. Proteins. 83: 1665-76. PMID 26138282 DOI: 10.1002/Prot.24852  0.478
2015 Wakefield AE, Wuest WM, Voelz VA. Molecular Simulation of Conformational Pre-Organization in Cyclic RGD Peptides. Journal of Chemical Information and Modeling. 55: 806-13. PMID 25741627 DOI: 10.1021/Ci500768U  0.464
2015 Voelz VA, Razavi A. Using Kinetic Network Models to Understand Folding Mechanisms of GB1 Hairpin and its Trpzip Variants Biophysical Journal. 108: 519a. DOI: 10.1016/J.Bpj.2014.11.2842  0.446
2015 Razavi AM, Carnevale V, Delemotte L, Voelz VA. Understanding Selectivity of the Na+/K+ -ATPase using a Computational Approach Biophysical Journal. 108: 197a. DOI: 10.1016/J.Bpj.2014.11.1087  0.329
2014 Voelz VA, Elman B, Razavi AM, Zhou G. Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State Models. Journal of Chemical Theory and Computation. 10: 5716-28. PMID 26583253 DOI: 10.1021/Ct500827G  0.38
2014 Voelz VA, Zhou G. Bayesian inference of conformational state populations from computational models and sparse experimental observables. Journal of Computational Chemistry. 35: 2215-24. PMID 25250719 DOI: 10.1002/Jcc.23738  0.465
2014 Razavi AM, Wuest WM, Voelz VA. Computational screening and selection of cyclic peptide hairpin mimetics by molecular simulation and kinetic network models. Journal of Chemical Information and Modeling. 54: 1425-32. PMID 24754484 DOI: 10.1021/Ci500102Y  0.486
2014 Baiz CR, Lin YS, Peng CS, Beauchamp KA, Voelz VA, Pande VS, Tokmakoff A. A molecular interpretation of 2D IR protein folding experiments with Markov state models. Biophysical Journal. 106: 1359-70. PMID 24655511 DOI: 10.1016/J.Bpj.2014.02.008  0.613
2013 Kortkhonjia E, Brandman R, Zhou JZ, Voelz VA, Chorny I, Kabakoff B, Patapoff TW, Dill KA, Swartz TE. Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations. Mabs. 5: 306-22. PMID 23396076 DOI: 10.4161/Mabs.23651  0.534
2013 Voelz VA, Zhou G, Elman B, Razavi Majarashin A, Delikatny ES. Examining Protein Sequence Perturbations with Markov State Models Biophysical Journal. 104: 226a. DOI: 10.1016/J.Bpj.2012.11.1276  0.426
2012 Butterfoss GL, Yoo B, Jaworski JN, Chorny I, Dill KA, Zuckermann RN, Bonneau R, Kirshenbaum K, Voelz VA. De novo structure prediction and experimental characterization of folded peptoid oligomers. Proceedings of the National Academy of Sciences of the United States of America. 109: 14320-5. PMID 22908242 DOI: 10.1073/Pnas.1209945109  0.597
2012 Voelz VA, Jäger M, Yao S, Chen Y, Zhu L, Waldauer SA, Bowman GR, Friedrichs M, Bakajin O, Lapidus LJ, Weiss S, Pande VS. Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. Journal of the American Chemical Society. 134: 12565-77. PMID 22747188 DOI: 10.1021/Ja302528Z  0.73
2012 Voelz VA, Pande VS. Calculation of rate spectra from noisy time series data Proteins: Structure, Function and Bioinformatics. 80: 342-351. PMID 22095854 DOI: 10.1002/Prot.23171  0.521
2011 Lane TJ, Bowman GR, Beauchamp K, Voelz VA, Pande VS. Markov State model reveals folding and functional dynamics in ultra-long MD trajectories Journal of the American Chemical Society. 133: 18413-18419. PMID 21988563 DOI: 10.1021/Ja207470H  0.724
2011 Voelz VA, Dill KA, Chorny I. Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER. Biopolymers. 96: 639-50. PMID 21184487 DOI: 10.1002/Bip.21575  0.598
2011 Bowman GR, Voelz VA, Pande VS. Atomistic folding simulations of the five-helix bundle protein λ 6-85 Journal of the American Chemical Society. 133: 664-667. PMID 21174461 DOI: 10.1021/Ja106936N  0.734
2011 Bowman GR, Voelz VA, Pande VS. Taming the complexity of protein folding Current Opinion in Structural Biology. 21: 4-11. PMID 21081274 DOI: 10.1016/J.Sbi.2010.10.006  0.701
2011 Voelz VA, Jäger M, Zhu L, Yao S, Bakajin O, Weiss S, Lapidus LJ, Pande VS. Markov State Models of Millisecond Folder ACBP Reveals New Views of the Folding Reaction Biophysical Journal. 100: 515a. DOI: 10.1016/J.Bpj.2010.12.3015  0.617
2011 Zhu L, Voelz VA, Bakajin O, Pande VS, Lapidus LJ. Revealing the Early Events of ACBP Folding by Ultrarapid Mixing Biophysical Journal. 100: 396a. DOI: 10.1016/J.Bpj.2010.12.2353  0.601
2011 Chen Y, Voelz VA, Bakajin O, Pande VS, Lapidus LJ. Diffusion of Unfolded Acyl-Coenzyme A-Binding Protein Over a Complete Range of Denaturant Biophysical Journal. 100: 211a. DOI: 10.1016/J.Bpj.2010.12.1362  0.563
2010 Voelz VA, Singh VR, Wedemeyer WJ, Lapidus LJ, Pande VS. Unfolded-state dynamics and structure of protein L characterized by simulation and experiment. Journal of the American Chemical Society. 132: 4702-9. PMID 20218718 DOI: 10.1021/Ja908369H  0.627
2010 Voelz VA, Bowman GR, Beauchamp K, Pande VS. Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). Journal of the American Chemical Society. 132: 1526-8. PMID 20070076 DOI: 10.1021/Ja9090353  0.74
2009 Voelz VA, Luttmann E, Bowman GR, Pande VS. Probing the nanosecond dynamics of a designed three-stranded beta-sheet with a massively parallel molecular dynamics simulation. International Journal of Molecular Sciences. 10: 1013-30. PMID 19399235 DOI: 10.3390/Ijms10031013  0.689
2009 Voelz VA, Petrone P, Pande VS. A multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnel. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 340-52. PMID 19209713  0.519
2009 Voelz VA, Shell MS, Dill KA. Predicting peptide structures in native proteins from physical simulations of fragments. Plos Computational Biology. 5: e1000281. PMID 19197352 DOI: 10.1371/Journal.Pcbi.1000281  0.633
2009 Shell MS, Ozkan SB, Voelz V, Wu GA, Dill KA. Blind test of physics-based prediction of protein structures. Biophysical Journal. 96: 917-24. PMID 19186130 DOI: 10.1016/J.Bpj.2008.11.009  0.747
2007 Dill KA, Ozkan SB, Weikl TR, Chodera JD, Voelz VA. The protein folding problem: when will it be solved? Current Opinion in Structural Biology. 17: 342-6. PMID 17572080 DOI: 10.1016/J.Sbi.2007.06.001  0.772
2007 Voelz VA, Dill KA. Exploring zipping and assembly as a protein folding principle. Proteins. 66: 877-88. PMID 17154424 DOI: 10.1002/Prot.21234  0.548
2003 Sullivan DC, Aynechi T, Voelz VA, Kuntz ID. Information content of molecular structures. Biophysical Journal. 85: 174-90. PMID 12829474 DOI: 10.1016/S0006-3495(03)74464-6  0.305
2002 LaConte LE, Voelz V, Nelson W, Enz M, Thomas DD. Molecular dynamics simulation of site-directed spin labeling: experimental validation in muscle fibers. Biophysical Journal. 83: 1854-66. PMID 12324407 DOI: 10.1016/S0006-3495(02)73950-7  0.329
2001 Cramer CJ, Kormos BL, Winget P, Audette VM, Beebe JM, Brauer CS, Burdick WR, Cochran EW, Eklov BL, Giese TJ, Jun Y, Kesavan LSD, Kinsinger CR, Minyaev ME, Rajamani R, ... ... Voelz VA, et al. A Cooperative Molecular Modeling Exercise—The Hypersurface as Classroom Journal of Chemical Education. 78: 1202. DOI: 10.1021/Ed078P1202  0.335
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