引用次数
引用: 1,038
H-指数: 16
I10-指数 : 20
出版物: 40
Towards a simplified model of the RNA free energy landscape and its Mg2+ dependence
Ryan Lee Hayes
Ph.D. Thesis
2015
Reduced Model Captures Mg2+-RNA Interaction Free Energy of Riboswitches
Ryan L. Hayes , Jeffrey K. Noel , Paul C. Whitford , Udayan Mohanty
Biophysical Journal 106 ( 7) 1508 -1519
33
2014
Intercellular Stress Reconstitution from Traction Force Data
Juliane Zimmermann , Ryan L. Hayes , Markus Basan , José N. Onuchic
Biophysical Journal 107 ( 3) 548 -554
26
2014
A strategy for proline and glycine mutations to proteins with alchemical free energy calculations.
Ryan L. Hayes , Charles L. Brooks
Journal of Computational Chemistry 42 ( 15) 1088 -1094
2021
Formation of Cosmic Dust Bunnies
Lorin S. Matthews , Ryan L. Hayes , Michael S. Freed , Truell W. Hyde
IEEE Transactions on Plasma Science 35 ( 2) 260 -265
22
2007
Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics.
Ryan L. Hayes , Kira A. Armacost , Jonah Z. Vilseck , Charles L. Brooks
Journal of Physical Chemistry B 121 ( 15) 3626 -3635
17
2017
Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.
Ryan L. Hayes , Jeffrey K. Noel , Ana Mandic , Paul C. Whitford
Physical Review Letters 114 ( 25) 258105 -258105
38
2015
Automated, Accurate, and Scalable Relative Protein–Ligand Binding Free-Energy Calculations Using Lambda Dynamics
E. Prabhu Raman , Thomas J. Paul , Ryan L. Hayes , Charles L. Brooks
Journal of Chemical Theory and Computation 16 ( 12) 7895 -7914
2
2020
Gibbs Sampler-Based λ-Dynamics and Rao–Blackwell Estimator for Alchemical Free Energy Calculation
Xinqiang Ding , Jonah Z. Vilseck , Ryan L. Hayes , Charles L. Brooks
Journal of Chemical Theory and Computation 13 ( 6) 2501 -2510
15
2017
Glass-Like Behavior of Magnesium Ions Inside RNA APTamers
Ryan L. Hayes , Jose Onuchic , Jeff Noel , Karissa Sanbonmatsu
Biophysical Journal 102 ( 3) 646a
2012
Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing.
Julia R. Widom , Yuri A. Nedialkov , Victoria Rai , Ryan L. Hayes
Molecular Cell 72 ( 3) 541 -552
16
2018
Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics.
Jonah Z. Vilseck , Kira A. Armacost , Ryan L. Hayes , Garrett B. Goh
Journal of Physical Chemistry Letters 9 ( 12) 3328 -3332
6
2018
Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1.
Jonah Z. Vilseck , Noor Sohail , Ryan L. Hayes , Charles L. Brooks
Journal of Physical Chemistry Letters 10 ( 17) 4875 -4880
16
2019
Approaching protein design with multisite λ dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme.
Ryan L. Hayes , Jonah Z. Vilseck , Charles L. Brooks
Protein Science 27 ( 11) 1910 -1922
5
2018
SMOG 2: A Versatile Software Package for Generating Structure-Based Models.
Jeffrey K. Noel , Mariana Levi , Mohit Raghunathan , Heiko Lammert
PLOS Computational Biology 12 ( 3)
106
2016
Exploring pH Dependent Host/Guest Binding Affinities.
Thomas J. Paul , Jonah Z. Vilseck , Ryan L. Hayes , Charles L. Brooks
Journal of Physical Chemistry B 124 ( 30) 6520 -6528
1
2020
Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch
Karissa Y. Sanbonmatsu , Ryan L. Hayes , Jeffrey K. Noel , Udayan Mohanty
Journal of the American Chemical Society 134 ( 29) 12043 -12053
60
2012
Structure-Based Model of RNA Pseudoknot Captures Magnesium-Dependent Folding Thermodynamics
Ana Mandic , Ryan L. Hayes , Heiko Lammert , Ryan R. Cheng
Journal of Physical Chemistry B 123 ( 7) 1505 -1511
4
2019
A magnesium-induced triplex pre-organizes the SAM-II riboswitch.
Susmita Roy , Heiko Lammert , Ryan L. Hayes , Bin Chen
PLOS Computational Biology 13 ( 3)
11
2017
Modeling traction forces in collective cell migration
Juliane Zimmermann , Markus Basan , Ryan L Hayes , Wouter-Jan Rappel
APS March Meeting Abstracts 2015 S49. 003 -S49. 003
2015