Jonah Z. Vilseck

发表

CDOCKER and $$\lambda$$λ-dynamics for prospective prediction in D3R Grand Challenge 2

Charles L. Brooks, Xinqiang Ding, Ryan L. Hayes, 2018, J. Comput. Aided Mol. Des..

Application of a BOSS—Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions

William L. Jorgensen, Jonah Z. Vilseck, Julian Tirado-Rives, 2015, J. Comput. Chem..

Optimal scaling factors for CM1 and CM3 atomic charges in RM1‐based aqueous simulations

Jonah Z. Vilseck, Orlando Acevedo, Somisetti V. Sambasivarao, 2011, J. Comput. Chem..

Mutant thermal proteome profiling for characterization of missense protein variants and their associated phenotypes within the proteome

Jonah Z. Vilseck, A. Mosley, Sarah A Peck Justice, 2020, The Journal of Biological Chemistry.

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning

Jonah Z. Vilseck, W. L. Jorgensen, M. Payne, 2016, Journal of chemical theory and computation.

Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.

Jonah Z. Vilseck, C. Brooks, R. L. Hayes, 2017, Journal of chemical theory and computation.

1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations.

William L. Jorgensen, Jonah Z. Vilseck, Julian Tirado-Rives, 2017, The journal of physical chemistry. B.

Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics.

Jonah Z. Vilseck, Kira A Armacost, Ryan L Hayes, 2017, The journal of physical chemistry. B.

Computing Free-Energy Profiles Using Multidimensional Potentials of Mean Force and Polynomial Quadrature Methods

Jonah Z. Vilseck, O. Acevedo, 2010 .

Approaching protein design with multisite λ dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme

Jonah Z. Vilseck, R. L. Hayes, Carl L Brooks, 2018, Protein science : a publication of the Protein Society.

Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics.

Jonah Z. Vilseck, C. Brooks, R. L. Hayes, 2018, The journal of physical chemistry letters.

Gas-Phase Ion/Ion Chemistry for Structurally Sensitive Probes of Gaseous Protein Ion Structure: Electrostatic and Electrostatic to Covalent Cross-Linking.

Jonah Z. Vilseck, Ian K. Webb, Melanie Cheung See Kit, 2020, International journal of mass spectrometry.

Generalizing the Discrete Gibbs Sampler-Based λ-Dynamics Approach for Multisite Sampling of Many Ligands.

Jonah Z. Vilseck, C. Brooks, R. L. Hayes, 2021, Journal of chemical theory and computation.

Substrate selectivity of the PRDM9 lysine methyltransferase domain

Jonah Z. Vilseck, A. Hudmon, E. Cornett, 2022, bioRxiv.

Regioselective synthesis of asymmetrically substituted 2-quinoxalinol salen ligands.

Jonah Z. Vilseck, Xianghong Wu, A. Gorden, 2007, Journal of Organic Chemistry.

Regioselective Synthesis of Asymmetrically Substituted 2‐Quinoxalinol Salen Ligands.

Jonah Z. Vilseck, Xianghong Wu, A. Gorden, 2008 .

Evaluation of CM5 Charges for Nonaqueous Condensed-Phase Modeling.

Jonah Z. Vilseck, William L Jorgensen, Leela S. Dodda, 2015, Journal of chemical theory and computation.

Determination of partial molar volumes from free energy perturbation theory.

Jonah Z. Vilseck, W. L. Jorgensen, J. Tirado-Rives, 2015, Physical chemistry chemical physics : PCCP.

Evaluation of CM5 Charges for Condensed-Phase Modeling

Jonah Z. Vilseck, W. L. Jorgensen, J. Tirado-Rives, 2014, Journal of chemical theory and computation.

Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization

Jonah Z. Vilseck, C. Brooks, R. L. Hayes, 2022, J. Chem. Inf. Model..

Accelerated CDOCKER with GPUs, parallel simulated annealing and fast Fourier transforms.

Jonah Z. Vilseck, C. Brooks, Xinqiang Ding, 2020, Journal of chemical theory and computation.

Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations.

Jonah Z. Vilseck, C. Brooks, Xinqiang Ding, 2019, Journal of chemical theory and computation.

Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods.

Jonah Z. Vilseck, R. L. Hayes, Carl L Brooks, 2022, Journal of chemical theory and computation.

Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1.

Jonah Z. Vilseck, C. Brooks, R. L. Hayes, 2019, The journal of physical chemistry letters.

Improved Cell-Potent and Selective Peptidomimetic Inhibitors of Protein N-Terminal Methyltransferase 1

Jonah Z. Vilseck, Rong Huang, Iredia D. Iyamu, 2022, Molecules.

Chemically induced partial unfolding of the multifunctional Apurinic/apyrimidinic endonuclease 1

Jonah Z. Vilseck, Steven M. Johnson, M. Georgiadis, 2023, bioRxiv.

Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Drug-like Inhibitor.

Jonah Z. Vilseck, W. L. Jorgensen, J. Tirado-Rives, 2019, The journal of physical chemistry. B.

Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding.

Jonah Z. Vilseck, Julian Tirado-Rives, William L Jorgensen, 2018, Journal of chemical theory and computation.

Identification of nonhistone substrates of the lysine methyltransferase PRDM9

Jonah Z. Vilseck, A. Hudmon, E. Cornett, 2023, The Journal of biological chemistry.

CDOCKER and λ -dynamics for prospective prediction in D3R Grand Challenge 2

Jonah Z. Vilseck, R. L. Hayes, Xinqiang Ding, 2018 .

Exploring pH Dependent Host/Guest Binding Affinities.

Jonah Z. Vilseck, Thomas J. Paul, C. Brooks, 2020, The journal of physical chemistry. B.

In silico λ-dynamics predicts protein binding specificities to modified RNAs

Jonah Z. Vilseck, Murphy Angelo, Wen Zhang, 2024, bioRxiv.