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Brian Radak
Brian Radak
Tandem AI
Verified email at tandemai.com
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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), 2020
18262020
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
2162020
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
1612017
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
1392020
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
1052013
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
862013
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
732014
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
682013
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
442020
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
402020
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), 2018
292018
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
292013
Accounting for the central role of interfacial water in protein–ligand binding free energy calculations
IY Ben-Shalom, Z Lin, BK Radak, C Lin, W Sherman, MK Gilson
Journal of chemical theory and computation 16 (12), 7883-7894, 2020
272020
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
272016
Multiscale methods for computational RNA enzymology
MT Panteva, T Dissanayake, H Chen, BK Radak, ER Kuechler, ...
Methods in enzymology 553, 335-374, 2015
272015
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
242015
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
232015
Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations
BK Radak, B Roux
The Journal of Chemical Physics 145 (13), 2016
202016
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
172009
Fast equilibration of water between buried sites and the bulk by molecular dynamics with parallel Monte Carlo water moves on graphical processing units
IY Ben-Shalom, C Lin, BK Radak, W Sherman, MK Gilson
Journal of chemical theory and computation 17 (12), 7366-7372, 2021
162021
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