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Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys

The journal of physical chemistry letters, 2018-08, Vol.9 (16), p.4738-4745

2018

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Revealing the Mechanism of Irreversible Binding of Antifreeze Glycoproteins to Ice

The journal of physical chemistry. B, 2022-12, Vol.126 (50), p.10637-10645

2022

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Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations

Nature protocols, 2022-04, Vol.17 (4), p.1114-1141

2022

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The lubricating role of water in the shuttling of rotaxanes

Chemical science (Cambridge), 2017-07, Vol.8 (7), p.5087-5094

2017

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Mechanism and biomass association of glucuronoyl esterase: an α/β hydrolase with potential in biomass conversion

Nature communications, 2022-03, Vol.13 (1), p.1449-1449, Article 1449

2022

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Sonoporation at Small and Large Length Scales: Effect of Cavitation Bubble Collapse on Membranes

The journal of physical chemistry letters, 2015-02, Vol.6 (3), p.413-418

2015

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PAS: Prediction-Based Actuation System for City-Scale Ridesharing Vehicular Mobile Crowdsensing

IEEE internet of things journal, 2020-05, Vol.7 (5), p.3719-3734

2020

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IEEE_Xplore

Unveiling the Hidden Movements in the Shuttling of Rotaxanes

Chemical research in Chinese universities, 2020-10, Vol.36 (5), p.748-754

2020

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Evaluating the Impact of User Behavior on D2D Communications in Millimeter-Wave Small Cells

IEEE transactions on vehicular technology, 2017-07, Vol.66 (7), p.6362-6377

2017

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IEEE_Xplore

Uncovering the Mechanism of Drug Resistance Caused by the T790M Mutation in EGFR Kinase From Absolute Binding Free Energy Calculations

Frontiers in molecular biosciences, 2022-05, Vol.9, p.922839-922839

2022

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Taming Rugged Free Energy Landscapes Using an Average Force

Accounts of chemical research, 2019-11, Vol.52 (11), p.3254-3264

2019

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Computer-aided design of molecular machines: techniques, paradigms and difficulties

Physical chemistry chemical physics : PCCP, 2022-01, Vol.24 (3), p.1286-1299

2022

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BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations

Journal of chemical information and modeling, 2021-05, Vol.61 (5), p.2116-2123

2021

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Meta-Analysis Reveals That Absolute Binding Free-Energy Calculations Approach Chemical Accuracy

Journal of medicinal chemistry, 2022-10, Vol.65 (19), p.12970-12978

2022

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Standard Binding Free-Energy Calculations: How Far Are We from Automation?

The journal of physical chemistry. B, 2023-12, Vol.127 (49), p.10459-10468

2023

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Understanding the Reversible Binding of a Multichain Protein–Protein Complex through Free-Energy Calculations

The journal of physical chemistry. B, 2024-04, Vol.128 (15), p.3598-3604

2024

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Analyzing Molecular Dynamics Trajectories Thermodynamically through Artificial Intelligence

Journal of chemical theory and computation, 2024-01, Vol.20 (2), p.665-676

2024

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Binding Thermodynamics of Fourth-Generation EGFR Inhibitors Revealed by Absolute Binding Free Energy Calculations

Journal of chemical information and modeling, 2023-12, Vol.63 (24), p.7837-7846

2023

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Collective Variable-Based Enhanced Sampling: From Human Learning to Machine Learning

The journal of physical chemistry letters, 2024-02, Vol.15 (6), p.1774-1783

2024

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Finding an Optimal Pathway on a Multidimensional Free-Energy Landscape

Journal of chemical information and modeling, 2020-11, Vol.60 (11), p.5366-5374

2020

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Overcoming Free-Energy Barriers with a Seamless Combination of a Biasing Force and a Collective Variable-Independent Boost Potential

Journal of chemical theory and computation, 2021-07, Vol.17 (7), p.3886-3894

2021

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Achieving Accurate Standard Protein–Protein Binding Free Energy Calculations through the Geometrical Route and Ergodic Sampling

Journal of chemical information and modeling, 2023-04, Vol.63 (8), p.2512-2519

2023

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Accurate Description of Cation−π Interactions in Proteins with a Nonpolarizable Force Field at No Additional Cost

Journal of chemical theory and computation, 2020-10, Vol.16 (10), p.6397-6407

2020

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Accuracy of Alternate Nonpolarizable Force Fields for the Determination of Protein–Ligand Binding Affinities Dominated by Cation−π Interactions

Journal of chemical theory and computation, 2021-07, Vol.17 (7), p.3908-3915

2021

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Accurate Description of Solvent-Exposed Salt Bridges with a Non-polarizable Force Field Incorporating Solvent Effects

Journal of chemical information and modeling, 2022-08, Vol.62 (16), p.3863-3873

2022

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Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys

Revealing the Mechanism of Irreversible Binding of Antifreeze Glycoproteins to Ice

Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations

The lubricating role of water in the shuttling of rotaxanes

Mechanism and biomass association of glucuronoyl esterase: an α/β hydrolase with potential in biomass conversion

Sonoporation at Small and Large Length Scales: Effect of Cavitation Bubble Collapse on Membranes

PAS: Prediction-Based Actuation System for City-Scale Ridesharing Vehicular Mobile Crowdsensing

Unveiling the Hidden Movements in the Shuttling of Rotaxanes

Evaluating the Impact of User Behavior on D2D Communications in Millimeter-Wave Small Cells

Uncovering the Mechanism of Drug Resistance Caused by the T790M Mutation in EGFR Kinase From Absolute Binding Free Energy Calculations

Taming Rugged Free Energy Landscapes Using an Average Force

Computer-aided design of molecular machines: techniques, paradigms and difficulties

BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations

Meta-Analysis Reveals That Absolute Binding Free-Energy Calculations Approach Chemical Accuracy

Standard Binding Free-Energy Calculations: How Far Are We from Automation?

Understanding the Reversible Binding of a Multichain Protein–Protein Complex through Free-Energy Calculations

Analyzing Molecular Dynamics Trajectories Thermodynamically through Artificial Intelligence

Binding Thermodynamics of Fourth-Generation EGFR Inhibitors Revealed by Absolute Binding Free Energy Calculations

Collective Variable-Based Enhanced Sampling: From Human Learning to Machine Learning

Finding an Optimal Pathway on a Multidimensional Free-Energy Landscape

Overcoming Free-Energy Barriers with a Seamless Combination of a Biasing Force and a Collective Variable-Independent Boost Potential

Achieving Accurate Standard Protein–Protein Binding Free Energy Calculations through the Geometrical Route and Ergodic Sampling

Accurate Description of Cation−π Interactions in Proteins with a Nonpolarizable Force Field at No Additional Cost

Accuracy of Alternate Nonpolarizable Force Fields for the Determination of Protein–Ligand Binding Affinities Dominated by Cation−π Interactions

Accurate Description of Solvent-Exposed Salt Bridges with a Non-polarizable Force Field Incorporating Solvent Effects

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