13 Publications
2019
Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor
Qian, Yue⋅Cabeza de Vaca, Israel⋅Vilseck, Jonah Z⋅Cole, Daniel J⋅Tirado-Rives, Julian and Jorgensen, William L
The journal of physical chemistry. B, vol. 123, (no. 41), pp. 8685, 2019-10-17. | Journal Article
 
Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1
Vilseck, Jonah Z⋅Sohail, Noor⋅Hayes, Ryan L and Brooks, 3rd, Charles L
The journal of physical chemistry letters, vol. 10, (no. 17), pp. 4880, 2019-Aug-13. | Journal Article
2018
Approaching protein design with multisite λ dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme
Hayes, Ryan L⋅Vilseck, Jonah Z and Brooks, Charles L
Protein Science, vol. 27, (no. 11), pp. 1922, November 2018. | Journal Article
 
CDOCKER and λ-dynamics for prospective prediction in D₃R Grand Challenge 2
Ding, Xinqiang⋅Hayes, Ryan L⋅Vilseck, Jonah Z⋅Charles, Murchtricia K and Brooks, 3rd, Charles L
Journal of computer-aided molecular design, vol. 32, (no. 1), pp. 102, 2018-01-00. | Journal Article
 
Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding
Cabeza de Vaca, Israel⋅Cabeza de Vaca, Israel⋅Qian, Yue⋅Qian, Yue⋅Vilseck, Jonah Z⋅Vilseck, Jonah Z⋅Tirado-Rives, Julian⋅Tirado-Rives, Julian⋅Jorgensen, William L and Jorgensen, William L
Journal of Chemical Theory and Computation, vol. 14, (no. 6), pp. 3288, 20180612. | Journal Article
 
Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics
Vilseck, Jonah Z⋅Armacost, Kira A⋅Hayes, Ryan L⋅Goh, Garrett B and Brooks, Charles L
The Journal of Physical Chemistry Letters, vol. 9, (no. 12), pp. 3332, 20180621. | Journal Article
2017
Adaptive landscape flattening accelerates sampling of alchemical space in multisite lamda dynamics
Hayes, Ryan⋅Armacost, Kira⋅Vilseck, Jonah and Brooks, Charles
Journal of Physical Chemistry B, vol. 121, (no. 15), pp. 3626, 20170420. | Journal Article
 
Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics
Hayes, Ryan L⋅Hayes, Ryan L⋅Armacost, Kira A⋅Armacost, Kira A⋅Vilseck, Jonah Z⋅Vilseck, Jonah Z⋅Brooks, Charles L and Brooks, Charles L
The Journal of Physical Chemistry B, vol. 121, (no. 15), pp. 3635, 20170420. | Journal Article
 
Gibbs Sampler-Based λ‑Dynamics and Rao–Blackwell Estimator for Alchemical Free Energy Calculation
Ding, Xinqiang⋅Vilseck, Jonah Z⋅Hayes, Ryan L and Brooks, Charles L
Journal of Chemical Theory and Computation, vol. 13, (no. 6), pp. 2510, 20170613. | Journal Article
2015
Application of a BOSS—Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions
Vilseck, Jonah Z⋅Vilseck, Jonah Z⋅Kostal, Jakub⋅Kostal, Jakub⋅Tirado-Rives, Julian⋅Tirado‐Rives, Julian⋅Jorgensen, William L and Jorgensen, William L
Journal of Computational Chemistry, vol. 36, (no. 27), pp. 2074, October 15, 2015. | Journal Article
 
Determination of partial molar volumes from free energy perturbation theory
Vilseck, Jonah Z⋅Tirado-Rives, Julian and Jorgensen, William L
Physical chemistry chemical physics : PCCP, vol. 17, (no. 13), pp. 8415, 2015-Apr-07. | Journal Article
 
Determination of partial molar volumes from free energy perturbation theoryElectronic supplementary information (ESI) available: Supplementary tables and figures have been provided containing detailed thermodynamic results for liquid densities as a function of pressure and partial molar volumes (8 pages). See DOI: 10.1039/c4cp05304d
Vilseck, Jonah Z⋅Tirado-Rives, Julian and Jorgensen, William L
(no. 13), pp. 8415, 20150318. | Journal Article
2012
ChemInform Abstract: Computing Free‐Energy Profiles Using Multidimensional Potentials of Mean Force and Polynomial Quadrature Methods
Vilseck, Jonah Z and Acevedo, Orlando
ChemInform, vol. 43, (no. 28), pp. no, July 10, 2012. | Journal Article