Brian Radak
Cited by
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Scalable molecular dynamics on CPU and GPU architectures with NAMD
JC Phillips, DJ Hardy, JDC Maia, JE Stone, JV Ribeiro, RC Bernardi, ...
The Journal of chemical physics 153 (4), 044130, 2020
A new maximum likelihood approach for free energy profile construction from molecular simulations
TS Lee, BK Radak, A Pabis, DM York
Journal of chemical theory and computation 9 (1), 153-164, 2013
Constant-pH molecular dynamics simulations for large biomolecular systems
BK Radak, C Chipot, D Suh, S Jo, W Jiang, JC Phillips, K Schulten, ...
Journal of chemical theory and computation 13 (12), 5933-5944, 2017
Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation
H Gu, S Zhang, KY Wong, BK Radak, T Dissanayake, DL Kellerman, ...
Proceedings of the National Academy of Sciences 110 (32), 13002-13007, 2013
A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields
TJ Giese, H Chen, T Dissanayake, GM Giambasu, H Heldenbrand, ...
Journal of chemical theory and computation 9 (3), 1417-1427, 2013
Roadmaps through free energy landscapes calculated using the multidimensional vFEP approach
TS Lee, BK Radak, M Huang, KY Wong, DM York
Journal of chemical theory and computation 10 (1), 24-34, 2014
Rigorous free energy simulations in virtual screening
Z Cournia, BK Allen, T Beuming, DA Pearlman, BK Radak, W Sherman
Journal of Chemical Information and Modeling 60 (9), 4153-4169, 2020
Molecular Simulations of RNA 2′-O-Transesterification Reaction Models in Solution
BK Radak, ME Harris, DM York
The Journal of Physical Chemistry B 117 (1), 94-103, 2013
A two-metal-ion-mediated conformational switching pathway for HDV ribozyme activation
TS Lee, BK Radak, ME Harris, DM York
ACS catalysis 6 (3), 1853-1869, 2016
Multiscale methods for computational RNA enzymology
MT Panteva, T Dissanayake, H Chen, BK Radak, ER Kuechler, ...
Methods in enzymology 553, 335-374, 2015
Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery
TS Lee, BK Allen, TJ Giese, Z Guo, P Li, C Lin, TD McGee Jr, ...
Journal of Chemical Information and Modeling 60 (11), 5595-5623, 2020
Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations
BK Radak, M Romanus, TS Lee, H Chen, M Huang, A Treikalis, ...
Journal of chemical theory and computation 11 (2), 373-377, 2015
Spontaneous H2 Loss through the Interaction of Squaric Acid Derivatives and BeH2
MM Montero‐Campillo, M Yáńez, AM Lamsabhi, O Mó
Chemistry–A European Journal 20 (18), 5309-5316, 2014
Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM
BK Radak, TS Lee, ME Harris, DM York
RNA 21 (9), 1566-1577, 2015
Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics–Monte Carlo propagator
D Suh, BK Radak, C Chipot, B Roux
The Journal of chemical physics 148 (1), 014101, 2018
Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations
BK Radak, B Roux
The Journal of chemical physics 145 (13), 134109, 2016
Modeling Reactive Scattering of F(2P) at a Liquid Squalane Interface: A Hybrid QM/MM Molecular Dynamics Study
BK Radak, S Yockel, D Kim, GC Schatz
The Journal of Physical Chemistry A 113 (26), 7218-7226, 2009
Improved alchemical free energy calculations with optimized smoothstep softcore potentials
TS Lee, Z Lin, BK Allen, C Lin, BK Radak, Y Tao, HC Tsai, W Sherman, ...
Journal of Chemical Theory and Computation 16 (9), 5512-5525, 2020
Boosting free-energy perturbation calculations with GPU-accelerated NAMD
H Chen, JDC Maia, BK Radak, DJ Hardy, W Cai, C Chipot, E Tajkhorshid
Journal of Chemical Information and Modeling 60 (11), 5301-5307, 2020
A framework for flexible and scalable replica-exchange on production distributed CI
BK Radak, M Romanus, E Gallicchio, TS Lee, O Weidner, NJ Deng, P He, ...
Proceedings of the Conference on Extreme Science and Engineering Discovery …, 2013
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Articles 1–20