Brian Radak
Title
Cited by
Cited by
Year
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
1952020
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
832013
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
752017
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
622013
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
552013
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
542014
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
362020
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
272013
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
232016
Multiscale methods for computational RNA enzymology
MT Panteva, T Dissanayake, H Chen, BK Radak, ER Kuechler, ...
Methods in enzymology 553, 335-374, 2015
232015
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
222020
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
222015
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
202014
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
172015
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
162018
Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations
BK Radak, B Roux
The Journal of chemical physics 145 (13), 134109, 2016
162016
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
152009
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
122020
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
92020
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
92013
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Articles 1–20