SMOG 2: A Versatile Software Package for Generating Structure-Based Models

Jeffrey K. Noel, Mariana Levi, Mohit Raghunathan, +4

PLoS Computational Biology

EngineeringStructural BioinformaticsModeling MethodMolecular BiologyComputer-aided Design +23

Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch

Ryan L. Hayes, Jeffrey K. Noel, Udayan Mohanty, +4

Journal of the American Chemical Society

EngineeringMolecular BiologyMolecular DynamicsOuter-sphere MgMolecular Simulation +14

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

Ryan L. Hayes, Jeffrey K. Noel, Ana Mandic, +4

Physical Review Letters

Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing

Julia R. Widom, Yuri A. Nedialkov, Victoria Rai, +4

Molecular Cell

Transcriptional RegulationProtein FoldingNatural SciencesMedicineRna Structure Prediction +4

Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics

Ryan L. Hayes, Kira A. Armacost, Jonah Z. Vilseck, +1

The Journal of Physical Chemistry B

EngineeringComputational ChemistryMolecular DynamicsMolecular ThermodynamicsNumerical Simulation +18

Automated, Accurate, and Scalable Relative Protein–Ligand Binding Free-Energy Calculations Using Lambda Dynamics

E. Prabhu Raman, Thomas J. Paul, Ryan L. Hayes, +1

Journal of Chemical Theory and Computation

EngineeringMolecular BiologyComputational ChemistryAnalytical UltracentrifugationMolecular Dynamics +16

Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes

Ryan R. Cheng, Olle Nordesjö, Ryan L. Hayes, +4

Molecular Biology and Evolution

BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations

Ryan L. Hayes, Joshua Buckner, Charles L. Brooks

Journal of Chemical Theory and Computation

EngineeringMolecular BiologyComputational ChemistryMolecular DynamicsMolecular Design +19

Reduced Model Captures Mg2+-RNA Interaction Free Energy of Riboswitches

Ryan L. Hayes, Jeffrey K. Noel, Paul C. Whitford, +3

Biophysical Journal

Natural SciencesProtein FoldingRna Structure PredictionRna BiologyMolecular Biology +1

Approaching protein design with multisite <i>λ</i> dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme

Ryan L. Hayes, Jonah Z. Vilseck, Charles L. Brooks

Protein Science

Free EnergyEngineeringBiomolecular Structure PredictionMolecular BiologyEnzyme Design +18