| SMOG 2: a versatile software package for generating structure-based models JK Noel, M Levi, M Raghunathan, H Lammert, RL Hayes, JN Onuchic, ... PLoS computational biology 12 (3), e1004794, 2016 | 250 | 2016 |
| Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch RL Hayes, JK Noel, U Mohanty, PC Whitford, SP Hennelly, JN Onuchic, ... Journal of the American Chemical Society 134 (29), 12043-12053, 2012 | 95 | 2012 |
| Generalized Manning condensation model captures the RNA ion atmosphere RL Hayes, JK Noel, A Mandic, PC Whitford, KY Sanbonmatsu, U Mohanty, ... Physical review letters 114 (25), 258105, 2015 | 62 | 2015 |
| Connecting the sequence-space of bacterial signaling proteins to phenotypes using coevolutionary landscapes RR Cheng, O Nordesjö, RL Hayes, H Levine, SC Flores, JN Onuchic, ... Molecular biology and evolution 33 (12), 3054-3064, 2016 | 61 | 2016 |
| Ligand modulates cross-coupling between riboswitch folding and transcriptional pausing JR Widom, YA Nedialkov, V Rai, RL Hayes, CL Brooks, I Artsimovitch, ... Molecular cell 72 (3), 541-552. e6, 2018 | 60 | 2018 |
| Adaptive landscape flattening accelerates sampling of alchemical space in multisite λ dynamics RL Hayes, KA Armacost, JZ Vilseck, CL Brooks III The Journal of Physical Chemistry B 121 (15), 3626-3635, 2017 | 60 | 2017 |
| Automated, accurate, and scalable relative protein–ligand binding free-energy calculations using lambda dynamics EP Raman, TJ Paul, RL Hayes, CL Brooks III Journal of chemical theory and computation 16 (12), 7895-7914, 2020 | 52 | 2020 |
| Reduced model captures Mg2+-RNA interaction free energy of riboswitches RL Hayes, JK Noel, PC Whitford, U Mohanty, KY Sanbonmatsu, ... Biophysical journal 106 (7), 1508-1519, 2014 | 48 | 2014 |
| Gibbs sampler-based λ-dynamics and Rao–Blackwell estimator for alchemical free energy calculation X Ding, JZ Vilseck, RL Hayes, CL Brooks III Journal of chemical theory and computation 13 (6), 2501-2510, 2017 | 37 | 2017 |
| Predicting binding free energies in a large combinatorial chemical space using multisite λ dynamics JZ Vilseck, KA Armacost, RL Hayes, GB Goh, CL Brooks III The journal of physical chemistry letters 9 (12), 3328-3332, 2018 | 31 | 2018 |
| Intercellular stress reconstitution from traction force data J Zimmermann, RL Hayes, M Basan, JN Onuchic, WJ Rappel, H Levine Biophysical journal 107 (3), 548-554, 2014 | 31 | 2014 |
| Formation of cosmic dust bunnies LS Matthews, RL Hayes, MS Freed, TW Hyde IEEE transactions on plasma science 35 (2), 260-265, 2007 | 29 | 2007 |
| Approaching protein design with multisite λ dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme RL Hayes, JZ Vilseck, CL Brooks III Protein Science 27 (11), 1910-1922, 2018 | 26 | 2018 |
| A magnesium-induced triplex pre-organizes the SAM-II riboswitch S Roy, H Lammert, RL Hayes, B Chen, R LeBlanc, TK Dayie, JN Onuchic, ... PLoS computational biology 13 (3), e1005406, 2017 | 26 | 2017 |
| BLaDE: A basic lambda dynamics engine for GPU-accelerated molecular dynamics free energy calculations RL Hayes, J Buckner, CL Brooks III Journal of chemical theory and computation 17 (11), 6799-6807, 2021 | 24 | 2021 |
| Overcoming challenging substituent perturbations with multisite λ-dynamics: a case study targeting β-secretase 1 JZ Vilseck, N Sohail, RL Hayes, CL Brooks III The journal of physical chemistry letters 10 (17), 4875-4880, 2019 | 21 | 2019 |
| A strategy for proline and glycine mutations to proteins with alchemical free energy calculations RL Hayes, CL Brooks III Journal of computational chemistry 42 (15), 1088-1094, 2021 | 12 | 2021 |
| Optimizing multisite λ-dynamics throughput with charge renormalization JZ Vilseck, LF Cervantes, RL Hayes, CL Brooks III Journal of chemical information and modeling 62 (6), 1479-1488, 2022 | 9 | 2022 |
| CDOCKER and -dynamics for prospective prediction in D3R Grand Challenge 2 X Ding, RL Hayes, JZ Vilseck, MK Charles, CL Brooks III Journal of computer-aided molecular design 32 (1), 89-102, 2018 | 9 | 2018 |
| Generalizing the discrete Gibbs sampler-based λ-dynamics approach for multisite sampling of many ligands JZ Vilseck, X Ding, RL Hayes, CL Brooks III Journal of chemical theory and computation 17 (7), 3895-3907, 2021 | 8 | 2021 |
Charles L. Brooks IIICyrus Levinthal Distinguished University Professor of Chemistry and Biophysics; Warner-Lambert/ParkeVerified email at umich.edu
