| 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 | 1821 | 2020 |
| 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 | 214 | 2020 |
| 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 | 161 | 2017 |
| 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 | 139 | 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 | 105 | 2013 |
| 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 | 86 | 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 | 73 | 2014 |
| 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 | 68 | 2013 |
| 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 | 44 | 2020 |
| 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 | 40 | 2020 |
| 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 | 29 | 2018 |
| 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 | 29 | 2013 |
| 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 | 27 | 2020 |
| 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 | 27 | 2016 |
| Multiscale methods for computational RNA enzymology MT Panteva, T Dissanayake, H Chen, BK Radak, ER Kuechler, ... Methods in enzymology 553, 335-374, 2015 | 27 | 2015 |
| 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 | 24 | 2015 |
| 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 | 23 | 2015 |
| Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations BK Radak, B Roux The Journal of Chemical Physics 145 (13), 2016 | 20 | 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 | 17 | 2009 |
| 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 | 16 | 2021 |
Benoit RouxProfessor of Biochemistry, The university of ChicagoVerified email at uchicago.edu
