SMOG 2: A Versatile Software Package for Generating Structure-Based Models von Noel, Jeffrey K, Levi, Mariana, Raghunathan, Mohit, Lammert, Heiko, Hayes, Ryan L, Onuchic, José N, Whitford, Paul C

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Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling von Robo, Michael T., Hayes, Ryan L., Ding, Xinqiang, Pulawski, Brian, Vilseck, Jonah Z.

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A magnesium-induced triplex pre-organizes the SAM-II riboswitch von Roy, Susmita, Lammert, Heiko, Hayes, Ryan L, Chen, Bin, LeBlanc, Regan, Dayie, T Kwaku, Onuchic, José N, Sanbonmatsu, Karissa Y

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Intercellular Stress Reconstitution from Traction Force Data von Zimmermann, Juliane, Hayes, Ryan L., Basan, Markus, Onuchic, José N., Rappel, Wouter-Jan, Levine, Herbert

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BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations von Hayes, Ryan L, Buckner, Joshua, Brooks, Charles L

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Automated, Accurate, and Scalable Relative Protein–Ligand Binding Free-Energy Calculations Using Lambda Dynamics von Raman, E. Prabhu, Paul, Thomas J, Hayes, Ryan L, Brooks, Charles L

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A strategy for proline and glycine mutations to proteins with alchemical free energy calculations von Hayes, Ryan L., Brooks, Charles L.

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Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design von Hayes, Ryan L, Nixon, Charlotte F, Marqusee, Susan, Brooks, 3rd, Charles L

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Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics von Hayes, Ryan L, Armacost, Kira A, Vilseck, Jonah Z, Brooks, Charles L

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Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing von Widom, Julia R, Nedialkov, Yuri A, Rai, Victoria, Hayes, Ryan L, Brooks, 3rd, Charles L, Artsimovitch, Irina, Walter, Nils G

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Optimizing Multisite λ‑Dynamics Throughput with Charge Renormalization von Vilseck, Jonah Z, Cervantes, Luis F, Hayes, Ryan L

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Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods von Hayes, Ryan L, Vilseck, Jonah Z

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Generalizing the Discrete Gibbs Sampler-Based λ‑Dynamics Approach for Multisite Sampling of Many Ligands von Vilseck, Jonah Z, Ding, Xinqiang, Hayes, Ryan L

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Exploring pH Dependent Host/Guest Binding Affinities von Paul, Thomas J, Vilseck, Jonah Z, Hayes, Ryan L, Brooks, Charles L

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Approaching protein design with multisite λ dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme von Hayes, Ryan L., Vilseck, Jonah Z., Brooks, Charles L.

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Overcoming Challenging Substituent Perturbations with Multisite λ‑Dynamics: A Case Study Targeting β‑Secretase 1 von Vilseck, Jonah Z, Sohail, Noor, Hayes, Ryan L

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Gibbs Sampler-Based λ‑Dynamics and Rao–Blackwell Estimator for Alchemical Free Energy Calculation von Ding, Xinqiang, Vilseck, Jonah Z, Hayes, Ryan L, Brooks, Charles L

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How to Sample Dozens of Substitutions per Site with λ Dynamics von Hayes, Ryan L., Cervantes, Luis F., Abad Santos, Justin Cruz, Samadi, Amirmasoud, Vilseck, Jonah Z., Brooks, Charles L.

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Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics von Vilseck, Jonah Z, Armacost, Kira A, Hayes, Ryan L, Goh, Garrett B, Brooks, Charles L

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Generalized Manning Condensation Model Captures the RNA Ion Atmosphere von Hayes, Ryan L, Noel, Jeffrey K, Mandic, Ana, Whitford, Paul C, Sanbonmatsu, Karissa Y, Mohanty, Udayan, Onuchic, José N

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