List of works - Stefan Boresch

A molecular dynamics study of WPD-loop flexibility in PTP1B.

scientific article published on 26 March 2007

A molecular dynamics study of the dielectric properties of aqueous solutions of alanine and alanine dipeptide

scientific article

A targeted molecular dynamics study of WPD loop movement in PTP1B.

scientific article published on 12 May 2006

Absolute hydration free energies of blocked amino acids: implications for protein solvation and stability

scientific article published on January 2013

Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching

scientific article published on 15 November 2018

Alchemical free energy calculations and multiple conformational substates

scientific article published in February 2005

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

scientific article published on 29 April 2022

Avoiding the van der Waals endpoint problem using serial atomic insertion

CHARMM: the biomolecular simulation program

scientific article

Comments on “Anomalous Dielectric Relaxation of Aqueous Protein Solutions” by Nilashis Nandi and Biman Bagchi (J. Phys. Chem. A1998,102, 8217)

Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations.

scientific article published on 10 January 2017

Comparative modeling of GABA(A) receptors: limits, insights, future developments.

scientific article

Comparative models of GABAA receptor extracellular and transmembrane domains: important insights in pharmacology and function.

scientific article

Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations

scientific article

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

scientific article published on 19 January 2013

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

scientific article published on 8 March 2017

Convergence of single-step free energy perturbation

article by Stefan Boresch & H. Lee Woodcock published 27 December 2016 in Molecular Physics

Dielectric properties of glucose and maltose solutions

Dielectric spectroscopy in aqueous solutions of oligosaccharides: Experiment meets simulation

Dummy Atoms in Alchemical Free Energy Calculations

scientific article published on 14 June 2021

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

scientific article published on 31 December 2010

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

scientific article published on 31 December 2010

Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes

scientific article published on 17 September 2014

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett’s Acceptance Ratio and Enveloping Distribution Sampling Methods

scientific article published on 03 July 2012

Evaluating the stability of pharmacophore features using molecular dynamics simulations

article

Free energy simulations: the meaning of the individual contributions from a component analysis

scientific article published in September 1994

Hydration free energies of amino acids: why side chain analog data are not enough

scientific article

Influence of the treatment of electrostatic interactions on the results of free energy calculations of dipolar systems

Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis

article

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

scientific article published on 11 February 2014

Nonadditive Monte Carlo Simulation of Liquid Hydrogen Chloride Difference Algorithm and Parallel Implementation

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

scientific article published on November 4, 2010

Rationalization of the dielectric properties of common three-site water models in terms of their force field parameters

article

SAR-Guided Scoring Function and Mutational Validation Reveal the Binding Mode of CGS-8216 at the α1+/γ2– Benzodiazepine Site

scientific article published on 08 August 2018

Simulation studies of the protein-water interface. I. Properties at the molecular resolution

Simulation studies of the protein-water interface. II. Properties at the mesoscopic resolution

Single molecule pulling with large time steps

scientific article published on 6 June 2007

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

scientific article published on 14 February 2019

The Role of Bonded Energy Terms in Free Energy Simulations - Insights from Analytical Results

The dielectric self-consistent field method. I. Highways, byways, and illustrative results

The dielectric self-consistent field method. II. Application to the study of finite range effects

The meaning of component analysis: decomposition of the free energy in terms of specific interactions

scientific article published in December 1995

Towards a better description and understanding of biomolecular solvation

scientific article published in April 1999

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

scientific article published in February 2014

Unexpected relative aqueous solubilities of a phosphotyrosine analogue and two phosphonate derivatives

scientific article published in April 2005

Unorthodox uses of Bennett's acceptance ratio method

Use of Interaction Energies in QM/MM Free Energy Simulations

scientific article published on 02 July 2019

Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems

scientific article published on 5 November 2015

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

scientific article

List of works by Stefan Boresch

A molecular dynamics study of WPD-loop flexibility in PTP1B.

A molecular dynamics study of the dielectric properties of aqueous solutions of alanine and alanine dipeptide

A targeted molecular dynamics study of WPD loop movement in PTP1B.

Absolute hydration free energies of blocked amino acids: implications for protein solvation and stability

Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching

Alchemical free energy calculations and multiple conformational substates

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

Avoiding the van der Waals endpoint problem using serial atomic insertion

CHARMM: the biomolecular simulation program

Comments on “Anomalous Dielectric Relaxation of Aqueous Protein Solutions” by Nilashis Nandi and Biman Bagchi (J. Phys. Chem. A1998,102, 8217)

Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations.

Comparative modeling of GABA(A) receptors: limits, insights, future developments.

Comparative models of GABAA receptor extracellular and transmembrane domains: important insights in pharmacology and function.

Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations

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

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

Convergence of single-step free energy perturbation

Dielectric properties of glucose and maltose solutions

Dielectric spectroscopy in aqueous solutions of oligosaccharides: Experiment meets simulation

Dummy Atoms in Alchemical Free Energy Calculations

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

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

Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett’s Acceptance Ratio and Enveloping Distribution Sampling Methods

Evaluating the stability of pharmacophore features using molecular dynamics simulations

Free energy simulations: the meaning of the individual contributions from a component analysis

Hydration free energies of amino acids: why side chain analog data are not enough

Influence of the treatment of electrostatic interactions on the results of free energy calculations of dipolar systems

Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis

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

Nonadditive Monte Carlo Simulation of Liquid Hydrogen Chloride Difference Algorithm and Parallel Implementation

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

Rationalization of the dielectric properties of common three-site water models in terms of their force field parameters

SAR-Guided Scoring Function and Mutational Validation Reveal the Binding Mode of CGS-8216 at the α1+/γ2– Benzodiazepine Site

Simulation studies of the protein-water interface. I. Properties at the molecular resolution

Simulation studies of the protein-water interface. II. Properties at the mesoscopic resolution

Single molecule pulling with large time steps

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

The Role of Bonded Energy Terms in Free Energy Simulations - Insights from Analytical Results

The dielectric self-consistent field method. I. Highways, byways, and illustrative results

The dielectric self-consistent field method. II. Application to the study of finite range effects

The meaning of component analysis: decomposition of the free energy in terms of specific interactions

Towards a better description and understanding of biomolecular solvation

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

Unexpected relative aqueous solubilities of a phosphotyrosine analogue and two phosphonate derivatives

Unorthodox uses of Bennett's acceptance ratio method

Use of Interaction Energies in QM/MM Free Energy Simulations

Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems

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