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Predicting Binding Free Energies: Frontiers and Benchmarks

Annual review of biophysics, 2017-05, Vol.46, p.531

2017

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Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

Annual review of biophysics, 2013-01, Vol.42 (1), p.121-142

2013

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Guidelines for the analysis of free energy calculations

Journal of computer-aided molecular design, 2015-05, Vol.29 (5), p.397-411

2015

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Perspective: Alchemical free energy calculations for drug discovery

The Journal of chemical physics, 2012-12, Vol.137 (23), p.230901-230901

2012

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Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

Journal of the American Chemical Society, 2015-02, Vol.137 (7), p.2695-2703

2015

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Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water

Journal of chemical theory and computation, 2016-08, Vol.12 (8), p.4015-4024

2016

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Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects

The Journal of chemical physics, 2013-11, Vol.139 (18), p.184103-184103

2013

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Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Journal of computer-aided molecular design, 2017-01, Vol.31 (1), p.147-161

2017

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An overview of the SAMPL8 host–guest binding challenge

Journal of computer-aided molecular design, 2022-10, Vol.36 (10), p.707-734

2022

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Alchemical free energy methods for drug discovery: progress and challenges

Current opinion in structural biology, 2011-04, Vol.21 (2), p.150-160

2011

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A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations

Current topics in medicinal chemistry, 2017-01, Vol.17 (23), p.2577

2017

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Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations

The Journal of chemical physics, 2007-12, Vol.127 (21), p.214108-214108

2007

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Current Status of the AMOEBA Polarizable Force Field

The journal of physical chemistry. B, 2010-03, Vol.114 (8), p.2549-2564

2010

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Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages

Journal of chemical theory and computation, 2018-11, Vol.14 (11), p.5567-5582

2018

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Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability

Journal of computational chemistry, 2020-01, Vol.41 (3), p.247-257

2020

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Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo

The journal of physical chemistry. B, 2018-05, Vol.122 (21), p.5579-5598

2018

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On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

The Journal of chemical physics, 2006-08, Vol.125 (8), p.084902-084902

2006

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An optimized chemical-genetic method for cell-specific metabolic labeling of RNA

Nature methods, 2020-03, Vol.17 (3), p.311

2020

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Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles

Journal of chemical theory and computation, 2009-09, Vol.5 (9), p.2486-2502

2009

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Temperature artifacts in protein structures bias ligand-binding predictions

Chemical science (Cambridge), 2021-09, Vol.12 (34), p.11275-11293

2021

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Lead optimization mapper: automating free energy calculations for lead optimization

Journal of computer-aided molecular design, 2013-09, Vol.27 (9), p.755-770

2013

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Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

Journal of computer-aided molecular design, 2010-04, Vol.24 (4), p.307-316

2010

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Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry

Journal of medicinal chemistry, 2008-02, Vol.51 (4), p.769-779

2008

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Predicting Absolute Ligand Binding Free Energies to a Simple Model Site

Journal of molecular biology, 2007-08, Vol.371 (4), p.1118-1134

2007

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Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

Journal of chemical theory and computation, 2007-07, Vol.3 (4), p.1231-1235

2007

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Predicting Binding Free Energies: Frontiers and Benchmarks

Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

Guidelines for the analysis of free energy calculations

Perspective: Alchemical free energy calculations for drug discovery

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

An overview of the SAMPL8 host–guest binding challenge

Alchemical free energy methods for drug discovery: progress and challenges

A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations

Current Status of the AMOEBA Polarizable Force Field

Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages

Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

An optimized chemical-genetic method for cell-specific metabolic labeling of RNA

Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles

Temperature artifacts in protein structures bias ligand-binding predictions

Lead optimization mapper: automating free energy calculations for lead optimization

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry

Predicting Absolute Ligand Binding Free Energies to a Simple Model Site

Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

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