Brian K. Radak

University of Illinois Urbana-Champaign — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

19h-index4.6kcitations42works4.02yr avg
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Research Topics

Protein Structure and Dynamics(25), Spectroscopy and Quantum Chemical Studies(17), RNA and protein synthesis mechanisms(10), Advanced Chemical Physics Studies(9), DNA and Nucleic Acid Chemistry(9)

Publications42 total

Simulating Biomolecules with the Variable Protonation State: A Tutorial for Constant-pH Molecular Dynamics in NAMD
The Journal of Physical Chemistry B·2025· 4 citedOpen Access
Precise Binding Free Energy Calculations for Multiple Molecules Using an Optimal Measurement Network of Pairwise Differences
Journal of Chemical Theory and Computation·2021· 12 cited
Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units
Journal of Chemical Theory and Computation·2021· 24 citedOpen Access
Fast Equilibration of Water between Buried Sites and Bulk by MD with Parallel Monte Carlo Water Moves on GPUs
2021· 2 citedOpen Access
Fast Equilibration of Water between Buried Sites and Bulk by MD with Parallel Monte Carlo Water Moves on GPUs
2021Open Access
Fast Equilibration of Water between Buried Sites and Bulk by MD with Parallel Monte Carlo Water Moves on GPUs
2021· 1 citedOpen Access
Fast Equilibration of Water between Buried Sites and Bulk by MD with Parallel Monte Carlo Water Moves on GPUs
2021Open Access
Precise binding free energy calculations for multiple molecules using an optimal measurement network of pairwise differences
arXiv (Cornell University)·2021· 1 citedOpen Access
Accounting for the Central Role of Interfacial Water in Protein–Ligand Binding Free Energy Calculations
Journal of Chemical Theory and Computation·2020· 45 citedOpen Access
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery
Journal of Chemical Information and Modeling·2020· 363 citedOpen Access
Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD
Journal of Chemical Information and Modeling·2020· 68 citedOpen Access
Scalable molecular dynamics on CPU and GPU architectures with NAMD
The Journal of Chemical Physics·2020· 3.1k citedOpen Access
Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations
2020· 2 citedOpen Access
Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations
2020· 6 citedOpen Access
Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials
Journal of Chemical Theory and Computation·2020· 67 citedOpen Access
Rigorous Free Energy Simulations in Virtual Screening
Journal of Chemical Information and Modeling·2020· 215 citedOpen Access
Finite-sample bias in free energy bridge estimators
The Journal of Chemical Physics·2019· 5 citedOpen Access
Protonation States and Conformations of Inositol and Phosphoinositol Phosphates from Molecular Simulations
Biophysical Journal·2019Open Access
Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems
Journal of Chemical Theory and Computation·2018· 6 citedOpen Access
A generalized linear response framework for expanded ensemble and replica exchange simulations
The Journal of Chemical Physics·2018· 9 citedOpen Access
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Frequent Co-authors

Darrin M. York(14), Woody Sherman(13), Tai‐Sung Lee(11), Charles Lin(10), Benoı̂t Roux(9), Ido Ben‐Shalom(8), Michael K. Gilson(8), Christophe Chipot(6), Thakshila Dissanayake(5), Michael E. Harris(5), J. C. Phillips(4), Bryce K. Allen(4), Donghyuk Suh(4), Ming Huang(4), George C. Schatz(4), Wei Jiang(3), Klaus Schulten(3), Timothy J. Giese(3), Pengfei Li(3), Sunhwan Jo(3)