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Bayesian regression and model selection for isothermal titration calorimetry with enantiomeric mixtures

PloS one, 2022-09, Vol.17 (9), p.e0273656-e0273656

2022

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Bayesian Regression Quantifies Uncertainty of Binding Parameters from Isothermal Titration Calorimetry More Accurately Than Error Propagation

International journal of molecular sciences, 2023-10, Vol.24 (20), p.15074

2023

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Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation

Proceedings of the National Academy of Sciences - PNAS, 2011-11, Vol.108 (45), p.E1009-E1018

2011

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Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

PloS one, 2018-09, Vol.13 (9), p.e0203224-e0203224

2018

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Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase

Biochemistry (Easton), 2017-08, Vol.56 (34), p.4559-4567

2017

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Learned mappings for targeted free energy perturbation between peptide conformations

The Journal of chemical physics, 2023-09, Vol.159 (12)

2023

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Simple Entropy Terms for End-Point Binding Free Energy Calculations

Journal of chemical theory and computation, 2018-11, Vol.14 (11), p.6035-6049

2018

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Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations

Journal of chemical theory and computation, 2017-06, Vol.13 (6), p.2930-2944

2017

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On Restraints in End‐Point Protein–Ligand Binding Free Energy Calculations

Journal of computational chemistry, 2020-03, Vol.41 (6), p.573-586

2020

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On the polarization of ligands by proteins

Physical chemistry chemical physics : PCCP, 2020-06, Vol.22 (21), p.1244-1257

2020

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The Influence of Macromolecular Crowding on HIV-1 Protease Internal Dynamics

Journal of the American Chemical Society, 2006-05, Vol.128 (18), p.6006-6007

2006

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Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles

Journal of chemical information and modeling, 2018-09, Vol.58 (9), p.1915-1925

2018

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Role of Subunit D in Ubiquinone-Binding Site of Vibrio cholerae NQR: Pocket Flexibility and Inhibitor Resistance

ACS omega, 2019-11, Vol.4 (21), p.19324-19331

2019

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Correction to Intermediate Thermodynamic States Contribute Equally to Free Energy Convergence: A Demonstration with Replica Exchange

Journal of chemical theory and computation, 2018-06, Vol.14 (6), p.3364-3364

2018

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Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling

Journal of chemical theory and computation, 2017-10, Vol.13 (10), p.4649-4659

2017

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Nonequilibrium path-ensemble averages for symmetric protocols

The Journal of chemical physics, 2019-11, Vol.151 (19), p.194103-194103

2019

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Intermediate Thermodynamic States Contribute Equally to Free Energy Convergence: A Demonstration with Replica Exchange

Journal of chemical theory and computation, 2016-05, Vol.12 (5), p.2154-2161

2016

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Remarkable Loop Flexibility in Avian Influenza N1 and Its Implications for Antiviral Drug Design

Journal of the American Chemical Society, 2007-06, Vol.129 (25), p.7764-7765

2007

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On Inactivation of the Coronavirus Main Protease

Journal of chemical information and modeling, 2024-03, Vol.64 (5), p.1644-1656

2024

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Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors

Journal of computational chemistry, 2020-03, Vol.41 (7), p.715-730

Minh, David D. L.

2020

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Understanding the Hastings Algorithm

Communications in statistics. Simulation and computation, 2015-01, Vol.44 (2), p.332-349

2015

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Inclusion of Control Data in Fits to Concentration–Response Curves Improves Estimates of Half-Maximal Concentrations

Journal of medicinal chemistry, 2023-09, Vol.66 (18), p.12751-12761

2023

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Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease

The journal of physical chemistry letters, 2010-01, Vol.1 (1), p.107-110

2010

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Springs and Speeds in Free Energy Reconstruction from Irreversible Single-Molecule Pulling Experiments

The journal of physical chemistry. B, 2008-05, Vol.112 (19), p.5892-5897

2008

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Power transformations improve interpolation of grids for molecular mechanics interaction energies

Journal of computational chemistry, 2018-07, Vol.39 (19), p.1200-1207

Minh, David D. L.

2018

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Bayesian regression and model selection for isothermal titration calorimetry with enantiomeric mixtures

Bayesian Regression Quantifies Uncertainty of Binding Parameters from Isothermal Titration Calorimetry More Accurately Than Error Propagation

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase

Learned mappings for targeted free energy perturbation between peptide conformations

Simple Entropy Terms for End-Point Binding Free Energy Calculations

Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations

On Restraints in End‐Point Protein–Ligand Binding Free Energy Calculations

On the polarization of ligands by proteins

The Influence of Macromolecular Crowding on HIV-1 Protease Internal Dynamics

Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles

Role of Subunit D in Ubiquinone-Binding Site of Vibrio cholerae NQR: Pocket Flexibility and Inhibitor Resistance

Correction to Intermediate Thermodynamic States Contribute Equally to Free Energy Convergence: A Demonstration with Replica Exchange

Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling

Nonequilibrium path-ensemble averages for symmetric protocols

Intermediate Thermodynamic States Contribute Equally to Free Energy Convergence: A Demonstration with Replica Exchange

Remarkable Loop Flexibility in Avian Influenza N1 and Its Implications for Antiviral Drug Design

On Inactivation of the Coronavirus Main Protease

Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors

Understanding the Hastings Algorithm

Inclusion of Control Data in Fits to Concentration–Response Curves Improves Estimates of Half-Maximal Concentrations

Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease

Springs and Speeds in Free Energy Reconstruction from Irreversible Single-Molecule Pulling Experiments

Power transformations improve interpolation of grids for molecular mechanics interaction energies

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