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

PLoS computational biology, 2016-03, Vol.12 (3), p.e1004794-e1004794

2016

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Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling

Nature communications, 2023-12, Vol.14 (1), p.8515-8515, Article 8515

2023

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A magnesium-induced triplex pre-organizes the SAM-II riboswitch

PLoS computational biology, 2017-03, Vol.13 (3), p.e1005406-e1005406

2017

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Intercellular Stress Reconstitution from Traction Force Data

Biophysical journal, 2014-08, Vol.107 (3), p.548-554

2014

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

Journal of chemical theory and computation, 2021-11, Vol.17 (11), p.6799-6807

2021

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

Journal of chemical theory and computation, 2020-12, Vol.16 (12), p.7895-7914

2020

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A strategy for proline and glycine mutations to proteins with alchemical free energy calculations

Journal of computational chemistry, 2021-06, Vol.42 (15), p.1088-1094

2021

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

The journal of physical chemistry. B, 2017-04, Vol.121 (15), p.3626-3635

2017

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Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design

Proceedings of the National Academy of Sciences - PNAS, 2024-01, Vol.121 (3), p.e2312029121

2024

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Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing

Molecular cell, 2018-11, Vol.72 (3), p.541-552.e6

2018

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Optimizing Multisite λ‑Dynamics Throughput with Charge Renormalization

Journal of chemical information and modeling, 2022-03, Vol.62 (6), p.1479-1488

2022

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Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods

Journal of chemical theory and computation, 2022-04, Vol.18 (4), p.2114-2123

2022

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Exploring pH Dependent Host/Guest Binding Affinities

The journal of physical chemistry. B, 2020-07, Vol.124 (30), p.6520-6528

2020

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Generalizing the Discrete Gibbs Sampler-Based λ‑Dynamics Approach for Multisite Sampling of Many Ligands

Journal of chemical theory and computation, 2021-07, Vol.17 (7), p.3895-3907

2021

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How to Sample Dozens of Substitutions per Site with λ Dynamics

Journal of chemical theory and computation, 2024-07, Vol.20 (14), p.6098-6110

2024

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

Protein science, 2018-11, Vol.27 (11), p.1910-1922

2018

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Overcoming Challenging Substituent Perturbations with Multisite λ‑Dynamics: A Case Study Targeting β‑Secretase 1

The journal of physical chemistry letters, 2019-09, Vol.10 (17), p.4875-4880

2019

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Gibbs Sampler-Based λ‑Dynamics and Rao–Blackwell Estimator for Alchemical Free Energy Calculation

Journal of chemical theory and computation, 2017-06, Vol.13 (6), p.2501-2510

2017

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Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

Physical review letters, 2015-06, Vol.114 (25), Article 258105

2015

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Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics

The journal of physical chemistry letters, 2018-06, Vol.9 (12), p.3328-3332

2018

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Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

Physical review letters, 2015-06, Vol.114 (25), p.258105-258105

2015

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Structure-Based Model of RNA Pseudoknot Captures Magnesium-Dependent Folding Thermodynamics

The journal of physical chemistry. B, 2019-02, Vol.123 (7), p.1505-1511

2019

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Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches

Biophysical journal, 2014-04, Vol.106 (7), p.1508-1519

2014

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

Biophysical journal, 2014-04, Vol.106 (7), p.1508-1519

2014

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CDOCKER and λ-dynamics for prospective prediction in D3R Grand Challenge 2

Journal of computer-aided molecular design, 2018-01, Vol.32 (1), p.89-102

2018

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

Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling

A magnesium-induced triplex pre-organizes the SAM-II riboswitch

Intercellular Stress Reconstitution from Traction Force Data

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

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

A strategy for proline and glycine mutations to proteins with alchemical free energy calculations

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

Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design

Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing

Optimizing Multisite λ‑Dynamics Throughput with Charge Renormalization

Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods

Exploring pH Dependent Host/Guest Binding Affinities

Generalizing the Discrete Gibbs Sampler-Based λ‑Dynamics Approach for Multisite Sampling of Many Ligands

How to Sample Dozens of Substitutions per Site with λ Dynamics

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

Overcoming Challenging Substituent Perturbations with Multisite λ‑Dynamics: A Case Study Targeting β‑Secretase 1

Gibbs Sampler-Based λ‑Dynamics and Rao–Blackwell Estimator for Alchemical Free Energy Calculation

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

Structure-Based Model of RNA Pseudoknot Captures Magnesium-Dependent Folding Thermodynamics

Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches

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

CDOCKER and λ-dynamics for prospective prediction in D3R Grand Challenge 2

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