B. Radak

发表

Finite-sample bias in free energy bridge estimators.

B. Radak, 2019, The Journal of chemical physics.

Multiscale methods for computational RNA enzymology.

Maria T. Panteva, D. York, Tai-Sung Lee, 2015, Methods in enzymology.

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations.

M. Gilson, W. Sherman, Zhixiong Lin, 2020, Journal of chemical theory and computation.

Molecular simulations of RNA 2'-O-transesterification reaction models in solution.

Darrin M York, Brian K Radak, D. York, 2013, The journal of physical chemistry. B.

Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM

Tai-Sung Lee, Darrin M York, Brian K Radak, 2015, RNA.

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

Pengfei Li, Woody Sherman, Tai-Sung Lee, 2020, J. Chem. Inf. Model..

Scalable molecular dynamics on CPU and GPU architectures with NAMD.

Yi Wang, Aleksei Aksimentiev, Klaus Schulten, 2020, The Journal of chemical physics.

Fast Equilibration of Water between Buried Sites and Bulk by MD with Parallel Monte Carlo Water Moves on GPUs

M. Gilson, W. Sherman, I. Ben-Shalom, 2021 .

Rigorous Free Energy Simulations in Virtual Screening

Woody Sherman, Zoe Cournia, Thijs Beuming, 2020, J. Chem. Inf. Model..

Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach.

Tai-Sung Lee, Darrin M York, Ming Huang, 2014, Journal of chemical theory and computation.

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations.

Tai-Sung Lee, Darrin M York, Brian K Radak, 2013, Journal of chemical theory and computation.

A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields.

Tai-Sung Lee, Darrin M York, Ming Huang, 2013, Journal of chemical theory and computation.

Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation

Darrin M. York, Masaru Miyagi, Hong Gu, 2013, Proceedings of the National Academy of Sciences.

Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units.

M. Gilson, W. Sherman, I. Ben-Shalom, 2021, Journal of Chemical Theory and Computation.

Precise Binding Free Energy Calculations for Multiple Molecules Using an Optimal Measurement Network of Pairwise Differences.

Bryce K. Allen, W. Sherman, Huafeng Xu, 2021, Journal of chemical theory and computation.

Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD

David Joseph Hardy, David J. Hardy, Haochuan Chen, 2020, J. Chem. Inf. Model..

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Klaus Schulten, James C. Phillips, Sunhwan Jo, 2017, Journal of chemical theory and computation.

A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.

Tai-Sung Lee, Darrin M York, Brian K Radak, 2016, ACS catalysis.

Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials.

Woody Sherman, Tai-Sung Lee, Darrin M York, 2020, Journal of chemical theory and computation.

A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations.

Tai-Sung Lee, Darrin M York, Ming Huang, 2017, Journal of chemical theory and computation.

Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations.

Benoît Roux, Brian K Radak, B. Roux, 2016, The Journal of chemical physics.

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator.

C. Chipot, B. Roux, B. Radak, 2018, The Journal of chemical physics.

A generalized linear response framework for expanded ensemble and replica exchange simulations.

Donghyuk Suh, Benoît Roux, Brian K Radak, 2018, The Journal of chemical physics.

A framework for flexible and scalable replica-exchange on production distributed CI

Wei Dai, Shantenu Jha, Melissa Romanus, 2013, XSEDE.