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List of works by Brian K Radak

A Multi-dimensional B-spline Method for Accurate Modeling Sugar Puckering in QM/MM Simulations

scientific article

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

scientific article published on 12 December 2012

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

scientific article (publication date: 2016)

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

scientific article published on 01 August 2018

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

scientific article published on 18 November 2020

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

scientific article published on 16 September 2020

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

scientific article

Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations

scientific article published on February 2015

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

scientific article

Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

scientific article published on 27 November 2018

Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations.

scientific article published on October 2016

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

scientific article

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

scientific article published on 11 November 2021

Finite-sample bias in free energy bridge estimators

scientific article published on 01 July 2019

Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials

scientific article published on 16 July 2020

Multiscale methods for computational RNA enzymology.

scientific article published on 22 January 2015

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

scientific article published on 06 December 2021

Rigorous Free Energy Simulations in Virtual Screening

scientific article published on 16 June 2020

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

scientific article published on January 2014

Scalable molecular dynamics on CPU and GPU architectures with NAMD ⬇️

scientific article published on 01 July 2020

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