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Polarizable molecular dynamics simulations of ionic liquids: Influence of temperature control

The Journal of chemical physics, 2020-03, Vol.152 (9), p.094105-094105

2020

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Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method

Journal of computational chemistry, 2011-05, Vol.32 (7), p.1303-1319

2011

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Transport and dielectric properties of water and the influence of coarse-graining: comparing BMW, SPC/E, and TIP3P models

The Journal of chemical physics, 2014-02, Vol.140 (6), p.064107-064107

2014

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Absolute Hydration Free Energies of Blocked Amino Acids: Implications for Protein Solvation and Stability

Biophysical journal, 2013-01, Vol.104 (2), p.453-462

2013

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On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations

Journal of chemical information and modeling, 2024-05, Vol.64 (9), p.3605-3609

Boresch, Stefan

2024

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Use of Interaction Energies in QM/MM Free Energy Simulations

Journal of chemical theory and computation, 2019-08, Vol.15 (8), p.4632-4645

2019

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Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes

Molecules (Basel, Switzerland), 2023-05, Vol.28 (10), p.4006

2023

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Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

Journal of chemical theory and computation, 2014-04, Vol.10 (4), p.1406-1419

2014

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Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations

Journal of chemical information and modeling, 2017-02, Vol.57 (2), p.365-385

2017

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Evaluating the stability of pharmacophore features using molecular dynamics simulations

Biochemical and biophysical research communications, 2016-02, Vol.470 (3), p.685-689

2016

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Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities

Journal of computational chemistry, 2017-06, Vol.38 (16), p.1376-1388

2017

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Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool

Frontiers in molecular biosciences, 2022-09, Vol.9, p.954638-954638

2022

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Avoiding the van der Waals endpoint problem using serial atomic insertion

Journal of computational chemistry, 2011-08, Vol.32 (11), p.2449-2458

2011

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Comparative Models of GABAA Receptor Extracellular and Transmembrane Domains: Important Insights in Pharmacology and Function

Molecular pharmacology, 2005-11, Vol.68 (5), p.1291

2005

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The Good, the Bad, and the Ugly: "HiPen", a New Dataset for Validating (S)QM/MM Free Energy Simulations

Molecules (Basel, Switzerland), 2019-02, Vol.24 (4), p.681

2019

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Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration

Journal of computational chemistry, 2011-05, Vol.32 (7), p.1320-1333

2011

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Dummy Atoms in Alchemical Free Energy Calculations

Journal of chemical theory and computation, 2021-07, Vol.17 (7), p.4403-4419

2021

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Alchemical free energy calculations and multiple conformational substates

The Journal of chemical physics, 2005-02, Vol.122 (8), p.84109-84109

2005

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The Role of Bonded Terms in Free Energy Simulations: 1. Theoretical Analysis

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 1999-01, Vol.103 (1), p.103-118

1999

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Calculations of Absolute Solvation Free Energies with TransformatoApplication to the FreeSolv Database Using the CGenFF Force Field

Journal of chemical theory and computation, 2023-09, Vol.19 (17), p.5988-5998

2023

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Web-based computational chemistry education with CHARMMing I: Lessons and tutorial

PLoS computational biology, 2014-07, Vol.10 (7), p.e1003719-e1003719

2014

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Comparison of thermodynamic integration and Bennett's acceptance ratio for calculating relative protein-ligand binding free energies

Journal of computational chemistry, 2013-05, Vol.34 (12), p.1024

2013

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Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program

Journal of computational chemistry, 2022-06, Vol.43 (17), p.1151-1160

2022

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Convergence of single-step free energy perturbation

Molecular physics, 2017-06, Vol.115 (9-12), p.1200-1213

2017

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Non-Boltzmann sampling and Bennett's acceptance ratio method: How to profit from bending the rules

Journal of computational chemistry, 2011-04, Vol.32 (6), p.1082-1090

2011

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Polarizable molecular dynamics simulations of ionic liquids: Influence of temperature control

Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method

Transport and dielectric properties of water and the influence of coarse-graining: comparing BMW, SPC/E, and TIP3P models

Absolute Hydration Free Energies of Blocked Amino Acids: Implications for Protein Solvation and Stability

On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations

Use of Interaction Energies in QM/MM Free Energy Simulations

Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes

Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations

Evaluating the stability of pharmacophore features using molecular dynamics simulations

Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities

Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool

Avoiding the van der Waals endpoint problem using serial atomic insertion

Comparative Models of GABAA Receptor Extracellular and Transmembrane Domains: Important Insights in Pharmacology and Function

The Good, the Bad, and the Ugly: "HiPen", a New Dataset for Validating (S)QM/MM Free Energy Simulations

Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration

Dummy Atoms in Alchemical Free Energy Calculations

Alchemical free energy calculations and multiple conformational substates

The Role of Bonded Terms in Free Energy Simulations: 1. Theoretical Analysis

Calculations of Absolute Solvation Free Energies with TransformatoApplication to the FreeSolv Database Using the CGenFF Force Field

Web-based computational chemistry education with CHARMMing I: Lessons and tutorial

Comparison of thermodynamic integration and Bennett's acceptance ratio for calculating relative protein-ligand binding free energies

Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program

Convergence of single-step free energy perturbation

Non-Boltzmann sampling and Bennett's acceptance ratio method: How to profit from bending the rules

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