Ryan Hayes
Ryan Hayes
Postdoctoral Fellow, University of Michigan
Verified email at pointloma.edu
Title
Cited by
Cited by
Year
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
1152016
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
702012
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
382014
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
362015
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
342016
Formation of cosmic dust bunnies
LS Matthews, RL Hayes, MS Freed, TW Hyde
IEEE transactions on plasma science 35 (2), 260-265, 2007
272007
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
262014
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
252017
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
192017
Ligand modulates cross-coupling between riboswitch folding and transcriptional pausing
JR Widom, YA Nedialkov, V Rai, RL Hayes, CL Brooks III, I Artsimovitch, ...
Molecular cell 72 (3), 541-552. e6, 2018
122018
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
102018
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
92017
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
72018
CDOCKER and -dynamics for prospective prediction in D3R Grand Challenge 2
X Ding, RL Hayes, JZ Vilseck, MK Charles, CL Brooks
Journal of computer-aided molecular design 32 (1), 89-102, 2018
52018
The Fractal Dimension and CHarging of Preplanetary Dust Aggregates
R Hayes, M Freed
Journal of Young Investigators, 2007
32007
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
22019
Structure-Based Model of RNA Pseudoknot Captures Magnesium-Dependent Folding Thermodynamics
A Mandic, RL Hayes, H Lammert, RR Cheng, JN Onuchic
The Journal of Physical Chemistry B 123 (7), 1505-1511, 2019
22019
Magnesium dependence of the RNA free energy landscape
RL Hayes, JK Noel, A Mandic, PC Whitford, KY Sanbonmatsu, U Mohanty, ...
Biophysical Journal 108 (2), 235a, 2015
22015
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
2020
Exploring pH Dependent Host/Guest Binding Affinities
TJ Paul, JZ Vilseck, RL Hayes, CL Brooks III
The Journal of Physical Chemistry B 124 (30), 6520-6528, 2020
2020
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Articles 1–20