Vincent A. Voelz

发表

BICePs 2.0: New Tools for Bayesian Inference of Conformational Populations from Theory and Experiment

Yunhui Ge, Robert M. Raddi, Vincent A. Voelz, 2020 .

Unveiling Ligand Binding Mechanisms through Molecular Simulation: Lessons and Progress from Markov State Model Approaches

Vincent A. Voelz, 2020 .

Binding of MDM2 Inhibitors via Biased Sampling and Multi-Ensemble Markov Models

Vincent A. Voelz, Matthew F. D. Hurley, 2020 .

Computational Screening and Selection of Cyclic Peptide Hairpin Mimetics by Molecular Simulation and Kinetic Network Models

Vincent A. Voelz, Asghar M. Razavi, William M. Wuest, 2014, J. Chem. Inf. Model..

Bayesian inference of conformational state populations from computational models and sparse experimental observables

Guangfeng Zhou, Vincent A. Voelz, Guangfeng Zhou, 2014, J. Comput. Chem..

Adaptive Markov state model estimation using short reseeding trajectories.

Hongbin Wan, Vincent A. Voelz, 2020, The Journal of chemical physics.

Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments

Ken A. Dill, M. Scott Shell, Vincent A. Voelz, 2009, PLoS Comput. Biol..

On the Use of Short Reseeding Trajectories to Sample Markov State Models

Hongbin Wan, Vincent A. Voelz, 2019 .

A Multiscale Approach to Sampling Nascent Peptide Chains in the Ribosomal Exit Tunnel

Vijay S. Pande, Vincent A. Voelz, P. Petrone, 2008, Pacific Symposium on Biocomputing.

Molecular Simulation of Conformational Pre-Organization in Cyclic RGD Peptides

Vincent A. Voelz, William M. Wuest, Amanda E. Wakefield, 2015, J. Chem. Inf. Model..

SARS-CoV-2 Simulations go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome

John D. Chodera, Vincent A. Voelz, Gregory R. Bowman, 2021, Biophysical Journal.

SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome

John D. Chodera, Vincent A. Voelz, Gregory R. Bowman, 2020, bioRxiv.

Stacking Gaussian processes to improve pKa predictions in the SAMPL7 challenge

Vincent A. Voelz, Robert M. Raddi, 2021, J. Comput. Aided Mol. Des..

Assigning confidence to molecular property prediction

AkshatKumar Nigam, Matteo Aldeghi, Al'an Aspuru-Guzik, 2021, Expert opinion on drug discovery.

Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution

Yunhui Ge, Vincent A. Voelz, Christian E. Schafmeister, 2021, J. Chem. Inf. Model..

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39).

Kyle A. Beauchamp, Vincent A. Voelz, V. Pande, 2010, Journal of the American Chemical Society.

Atomistic folding simulations of the five-helix bundle protein λ(6−85).

Vincent A. Voelz, V. Pande, G. Bowman, 2011, Journal of the American Chemical Society.

De novo structure prediction and experimental characterization of folded peptoid oligomers

Jonathan N. Jaworski, Vincent A. Voelz, Richard Bonneau, 2012, Proceedings of the National Academy of Sciences.

Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment.

Vincent A. Voelz, Lisa J. Lapidus, V. Pande, 2012, Journal of the American Chemical Society.

Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations

Vincent A. Voelz, K. Dill, Relly Brandman, 2013, mAbs.

Markov state model reveals folding and functional dynamics in ultra-long MD trajectories.

Kyle A. Beauchamp, Vincent A. Voelz, V. Pande, 2011, Journal of the American Chemical Society.

Computational and Experimental Evaluation of Designed β-Cap Hairpins Using Molecular Simulations and Kinetic Network Models

Vincent A. Voelz, N. Andersen, Yunhui Ge, 2017, J. Chem. Inf. Model..

Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding.

Vincent A. Voelz, Guangfeng Zhou, 2016, The journal of physical chemistry. B.

Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics

Vincent A. Voelz, George A. Pantelopulos, Sudipto Mukherjee, 2015, Proteins.

Kinetic network models of tryptophan mutations in β-hairpins reveal the importance of non-native interactions.

Vincent A. Voelz, Asghar M. Razavi, 2015, Journal of chemical theory and computation.

Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation

Vincent A. Voelz, V. Pande, Edgar Luttmann, 2009, International journal of molecular sciences.

Simulations of the regulatory ACT domain of human phenylalanine hydroxylase (PAH) unveil its mechanism of phenylalanine binding

Vincent A. Voelz, E. Jaffe, Yunhui Ge, 2018, The Journal of Biological Chemistry.

Open Science Discovery of Potent Non-Covalent SARS-CoV-2 Main Protease Inhibitors

Vincent A. Voelz, Matthew F. D. Hurley, R. Glen, 2020, bioRxiv.

Bridging microscopic and macroscopic mechanisms of p53-MDM2 binding using molecular simulations and kinetic network models

Vincent A. Voelz, George A. Pantelopulos, Sudipto Mukherjee, 2016, bioRxiv.

Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking

Vincent A. Voelz, George A. Pantelopulos, Sudipto Mukherjee, 2016, Scientific Reports.

Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network Models.

Vincent A. Voelz, George A. Pantelopulos, Sudipto Mukherjee, 2017, Biophysical journal.

Blind test of physics-based prediction of protein structures.

Vincent A. Voelz, K. Dill, S. Ozkan, 2009, Biophysical journal.

Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reaction

Vincent A. Voelz, Zakey Yusuf Buuh, Zhigang Lyu, 2020, Nature Communications.

Elucidating the inhibition of peptidoglycan biosynthesis in Staphylococcus aureus by albocycline, a macrolactone isolated from Streptomyces maizeus.

Guangfeng Zhou, Rodrigo B. Andrade, Yunhui Ge, 2018, Bioorganic & medicinal chemistry.

A molecular interpretation of 2D IR protein folding experiments with Markov state models.

Vincent A Voelz, Vijay S Pande, Kyle A Beauchamp, 2014, Biophysical journal.

Markov State Models of Millisecond Folder ACBP Reveals New Views of the Folding Reaction

Vijay S. Pande, Shimon Weiss, Vincent A. Voelz, 2011 .

Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking

Vincent A. Voelz, George A. Pantelopulos, Sudipto Mukherjee, 2016, bioRxiv.

Insights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential.

Vincent A. Voelz, Sudipto Mukherjee, Guangfeng Zhou, 2015, The journal of physical chemistry. B.

Information content of molecular structures.

D. C. Sullivan, Vincent A. Voelz, David C. Sullivan, 2003, Biophysical journal.

Site-Specific Immuno-PET Tracer to Image PD-L1.

Vincent A. Voelz, Emily B. Ehlerding, Sarah J. Bartlett, 2019, Molecular pharmaceutics.

Precisely tuneable energy transfer system using peptoid helix-based molecular scaffold

Vincent A. Voelz, Jiwon Seo, Sudipto Mukherjee, 2017, Scientific Reports.

Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2

Vincent A. Voelz, Yunhui Ge, Si Zhang, 2020, J. Chem. Inf. Model..

Control of porphyrin interactions via structural changes of a peptoid scaffold.

Vincent A. Voelz, Jiwon Seo, Woojin Yang, 2017, Organic & biomolecular chemistry.

Estimation of binding rates and affinities from multiensemble Markov models and ligand decoupling.

Vincent A. Voelz, Yunhui Ge, 2021, The Journal of chemical physics.

Diverted Total Synthesis of Carolacton-Inspired Analogs Yields Three Distinct Phenotypes in Streptococcus mutans Biofilms.

Vincent A. Voelz, R. Quivey, Guangfeng Zhou, 2017, Journal of the American Chemical Society.

Fluorinated Aromatic Monomers as Building Blocks To Control α-Peptoid Conformation and Structure.

Vincent A. Voelz, Matthew F. D. Hurley, J. Aguilar, 2019, Journal of the American Chemical Society.

Microcanonical coarse-graining of the kinetic Ising model.

Vincent A. Voelz, V. Carnevale, D. Sigg, 2020, The Journal of chemical physics.

Reconciling simulated ensembles of apomyoglobin with experimental HDX data using Bayesian inference and multi-ensemble Markov State Models

Vincent A. Voelz, Asghar M. Razavi, Yunhui Ge, 2019, bioRxiv.

Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies.

Michael R. Shirts, Vincent A. Voelz, David F. Hahn, 2021, Journal of chemical theory and computation.

A Cooperative Molecular Modeling Exercise— The Hypersurface as Classroom

Eric W. Cochran, Vincent A. Voelz, Timothy J. Giese, 2001 .

Effects of Salinity and Temperature on the Flexibility and Function of a Polyextremophilic Enzyme

Vincent A. Voelz, S. DasSarma, S. Solieva, 2022, International journal of molecular sciences.

Oncogenic mutations in the DNA-binding domain of FOXO1 disrupt folding: quantitative insights from experiments and molecular simulations

Vincent A. Voelz, Richard H. G. Baxter, Lei Qian, 2022, bioRxiv.

Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER.

Vincent A. Voelz, K. Dill, I. Chorny, 2011, Biopolymers.

Taming the complexity of protein folding.

Vincent A Voelz, Vijay S Pande, Gregory R Bowman, 2011, Current opinion in structural biology.

Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State Models.

Vincent A Voelz, Brandon Elman, Asghar M Razavi, 2014, Journal of chemical theory and computation.

Metal-Binding Q-Proline Macrocycles.

Vincent A. Voelz, Matthew F. D. Hurley, Michael J. Zdilla, 2021, The Journal of organic chemistry.

SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

Ivan G. Costa, Vincent A. Voelz, Matthew F. D. Hurley, 2021, Cell Stem Cell.

Molecular dynamics simulation of site-directed spin labeling: experimental validation in muscle fibers.

Vincent A. Voelz, David D. Thomas, L. LaConte, 2002, Biophysical journal.

The protein folding problem: when will it be solved?

S Banu Ozkan, Vincent A Voelz, Ken A Dill, 2007, Current opinion in structural biology.

Structure-Based Experimental Datasets for Benchmarking of Protein Simulation Force Fields

Vincent A. Voelz, D. Mobley, M. Wall, 2023, 2303.11056.

SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome

Vincent A. Voelz, Matthew F. D. Hurley, Rafal P. Wiewiora, 2021, Nature Chemistry.

Molecular simulations and free-energy calculations suggest conformation-dependent anion binding to a cytoplasmic site as a mechanism for Na+/K+-ATPase ion selectivity

Vincent A. Voelz, Asghar M. Razavi, V. Carnevale, 2017, The Journal of Biological Chemistry.

Free energy calculations suggest a mechanism for Na+/K+-ATPase ion selectivity

Vincent A. Voelz, Asghar M. Razavi, V. Carnevale, 2017, bioRxiv.

Precisely tuneable energy transfer system using peptoid helix-based molecular scaffold

Vincent A. Voelz, Jiwon Seo, Yoonsoo Pang, 2017, Scientific Reports.

Exploring zipping and assembly as a protein folding principle

Vincent A Voelz, Ken A Dill, Vincent A. Voelz, 2006, Proteins.

SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome

Vincent A. Voelz, Matthew F. D. Hurley, Rafal P. Wiewiora, 2020, Biophysical Journal.

Unfolded-state dynamics and structure of protein L characterized by simulation and experiment.

Vincent A Voelz, Vijay S Pande, Vincent A. Voelz, 2010, Journal of the American Chemical Society.

Open Science Discovery of Potent Non-Covalent SARS-CoV-2 Main Protease Inhibitors

David D. L. Minh, Vincent A. Voelz, Matthew F. D. Hurley, 2023, bioRxiv.

Markov State Models to Elucidate Ligand Binding Mechanism.

Vincent A. Voelz, Yunhui Ge, 2021, Methods in molecular biology.

Stacking Gaussian processes to improve pKa predictions in the SAMPL7 challenge

Vincent A. Voelz, Robert Raddi, Vincent Voelz, 2021, J. Comput. Aided Mol. Des..

Reconciling simulated ensembles of apomyoglobin with experimental HDX data using Bayesian inference and multi-ensemble Markov State Models.

Vincent A. Voelz, Asghar M. Razavi, Yunhui Ge, 2020, Journal of chemical theory and computation.

Folding@home: Achievements from over 20 years of citizen science herald the exascale era

Vincent A. Voelz, V. Pande, G. Bowman, 2023, Biophysical journal.

Reconciling Simulations and Experiments With BICePs: A Review

Vincent A. Voelz, Yunhui Ge, R. Raddi, 2021, Frontiers in Molecular Biosciences.

A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations.

Hongbin Wan, Vincent A Voelz, Guangfeng Zhou, 2016, Journal of chemical theory and computation.

BICePs v2.0: Software for Ensemble Reweighting Using Bayesian Inference of Conformational Populations

Vincent A. Voelz, Yunhui Ge, R. Raddi, 2023, J. Chem. Inf. Model..

Adaptive Markov state model estimation using short reseeding trajectories.

Vincent A. Voelz, Hongbin Wan, 2019, The Journal of chemical physics.

Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study.

Vincent A. Voelz, W. DeGrado, F. Gai, 2019, The journal of physical chemistry. B.

Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reaction

Vincent A. Voelz, Zakey Yusuf Buuh, Zhigang Lyu, 2022, Nature Communications.

Atomistic folding simulations of the five-helix bundle protein λ(6−85).

Vincent A. Voelz, V. Pande, G. Bowman, 2011, Journal of the American Chemical Society.

The protein folding problem: when will it be solved?

Vincent A. Voelz, J. Chodera, T. Weikl, 2007, Current opinion in structural biology.

Solution-state preorganization of cyclic � -hairpin ligands determines binding mechanism and a � nities

Vincent A. Voelz, Yunhui Ge, M. Erdélyi, 2021 .

Bayesian inference of conformational state populations from computational models and sparse experimental observables

Vincent A. Voelz, Guangfeng Zhou, 2014, J. Comput. Chem..

Drug Discovery in Low Data Regimes: Leveraging a Computational Pipeline for the Discovery of Novel SARS-CoV-2 Nsp14-MTase Inhibitors

Vincent A. Voelz, Matthew F. D. Hurley, A. Kundaje, 2023, bioRxiv.

SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

Ivan G. Costa, Vincent A. Voelz, Matthew F. D. Hurley, 2021, Cell Stem Cell.

Unfolded-state dynamics and structure of protein L characterized by simulation and experiment.

Vincent A. Voelz, Lisa J. Lapidus, V. Pande, 2010, Journal of the American Chemical Society.