List of works - Benoît Roux

A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls

scientific article published on 09 February 2022

A generalized linear response framework for expanded ensemble and replica exchange simulations

scientific article published on 01 August 2018

Amphiphile Induced Phase Transition of Liquid Crystals at Aqueous Interfaces

scientific article published on 22 October 2018

Atomic mutagenesis in ion channels with engineered stoichiometry

scientific article published on 6 October 2016

Biochemical patterns of antibody polyreactivity revealed through a bioinformatics-based analysis of CDR loops

scientific article published on 10 November 2020

CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations

scientific article published on 28 October 2020

Calculating the Effect of Membrane Thickness on the Lifetime of the Gramicidin A Channel: A Landmark

scientific article published on 10 October 2019

Challenges and Advantages of Accounting for Backbone Flexibility in Prediction of Protein–Protein Complexes

scientific article published on 25 February 2022

Characteristics of Impactful Computational Contributions to The Journal of Physical Chemistry B

scientific article published on 01 June 2020

Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg

scientific article published on 18 July 2018

Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD

scientific article published on 27 August 2019

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

scientific article

Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg"

scientific article published on 02 January 2019

Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

scientific article published on 27 November 2018

Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase

scientific article published on 05 March 2019

Crystal structure of an archaeal CorB magnesium transporter

scientific article published on 29 June 2021

Diversity of Long-Lived Intermediates along the Binding Pathway of Imatinib to Abl Kinase Revealed by MD Simulations

scientific article published on 04 November 2020

Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids

scientific article published on 21 July 2017

Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field

scientific article published on 06 October 2021

Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions.

scientific article published on 2 January 2018

H, N, and C resonance assignments of the intrinsically disordered SH4 and Unique domains of Hck

scientific article published on 04 October 2018

Hazardous Shortcuts in Standard Binding Free Energy Calculations

scientific article published in 2022

Identification of Druggable Kinase Target Conformations Using Markov Model Metastable States Analysis of apo-Abl

scientific article published on 13 February 2020

Machine Learning Force Field Parameters from Ab Initio Data.

scientific article published on 11 August 2017

Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches

scientific article published on 06 April 2022

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields

scientific article published on 29 May 2019

Molecular Dynamics of Ion Conduction Through the Selectivity Filter of the NavAb Sodium Channel

scientific article published on 29 October 2018

New Coarse Variables for the Accurate Determination of Standard Binding Free Energies

scientific article

Optimized Lennard-Jones Parameters for Drug-Like Small Molecules

scientific article

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator

scientific article published on 17 April 2018

Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel

scientific article published on 06 February 2021

Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models.

scientific article

Probing the Effects of Gating on the Ion Occupancy of the K+ Channel Selectivity Filter Using Two-Dimensional Infrared Spectroscopy

scientific article published on 5 May 2017

Rapid constriction of the selectivity filter underlies C-type inactivation in the KcsA potassium channel

scientific article published on 02 August 2018

Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis

scientific article published on 3 October 2018

Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software

scientific article published on 22 October 2018

Scalable molecular dynamics on CPU and GPU architectures with NAMD ⬇️

scientific article published on 01 July 2020

Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian

scientific article published on 01 September 2020

String Method for Protein-Protein Binding Free-Energy Calculations

scientific article published on 31 October 2019

The selectivity of the Na(+)/K(+)-pump is controlled by binding site protonation and self-correcting occlusion

scientific article published on 04 August 2016

Tyrosine Kinase Activation and Conformational Flexibility: Lessons from Src-Family Tyrosine Kinases.

scientific article published on 20 April 2017

Water Flux Induced Reorientation of Liquid Crystals

scientific article published on 15 December 2017

List of works by Benoît Roux

A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls

A generalized linear response framework for expanded ensemble and replica exchange simulations

Amphiphile Induced Phase Transition of Liquid Crystals at Aqueous Interfaces

Atomic mutagenesis in ion channels with engineered stoichiometry

Biochemical patterns of antibody polyreactivity revealed through a bioinformatics-based analysis of CDR loops

CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations

Calculating the Effect of Membrane Thickness on the Lifetime of the Gramicidin A Channel: A Landmark

Challenges and Advantages of Accounting for Backbone Flexibility in Prediction of Protein–Protein Complexes

Characteristics of Impactful Computational Contributions to The Journal of Physical Chemistry B

Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg

Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg"

Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase

Crystal structure of an archaeal CorB magnesium transporter

Diversity of Long-Lived Intermediates along the Binding Pathway of Imatinib to Abl Kinase Revealed by MD Simulations

Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids

Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field

Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions.

H, N, and C resonance assignments of the intrinsically disordered SH4 and Unique domains of Hck

Hazardous Shortcuts in Standard Binding Free Energy Calculations

Identification of Druggable Kinase Target Conformations Using Markov Model Metastable States Analysis of apo-Abl

Machine Learning Force Field Parameters from Ab Initio Data.

Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields

Molecular Dynamics of Ion Conduction Through the Selectivity Filter of the NavAb Sodium Channel

New Coarse Variables for the Accurate Determination of Standard Binding Free Energies

Optimized Lennard-Jones Parameters for Drug-Like Small Molecules

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator

Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel

Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models.

Probing the Effects of Gating on the Ion Occupancy of the K+ Channel Selectivity Filter Using Two-Dimensional Infrared Spectroscopy

Rapid constriction of the selectivity filter underlies C-type inactivation in the KcsA potassium channel

Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis

Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software

Scalable molecular dynamics on CPU and GPU architectures with NAMD ⬇️

Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian

String Method for Protein-Protein Binding Free-Energy Calculations

The selectivity of the Na(+)/K(+)-pump is controlled by binding site protonation and self-correcting occlusion

Tyrosine Kinase Activation and Conformational Flexibility: Lessons from Src-Family Tyrosine Kinases.

Water Flux Induced Reorientation of Liquid Crystals