Potential Energy Function for Cation-Peptide Interactions: An Ab Initio Study. - Benoît Roux; Martin Karplus (J. Comput. Chem., 1995)

A potential function for computer simulation studies of proton transfer in acetylacetone. - Konrad Hinsen; Benoît Roux (J. Comput. Chem., 1997)

Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational Energetics. - Jérôme Baudry; Serge Crouzy; Benoît Roux; Jeremy C. Smith (J. Chem. Inf. Comput. Sci., 1997)

Application of a Stochastic Path Integral Approach to the Computations of an Optimal Path and Ensembles of Trajectories. - Ron Elber; Benoît Roux; Roberto Olender (Computational Molecular Dynamics, 1999)

Efficient calculation of two-dimensional adiabatic and free energy maps: Application to the isomerization of the C13C14 and C15N16 bonds in the retinal of bacteriorhodopsin. - Serge Crouzy; Jérôme Baudry; Jeremy C. Smith; Benoît Roux (J. Comput. Chem., 1999)

Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects. - José D. Faraldo-Gómez; Benoît Roux (J. Comput. Chem., 2007)

PBEQ-Solver for online visualization of electrostatic potential of biomolecules. - Sunhwan Jo; Miklós Vargyas; Judit Vasko-Szedlar; Benoît Roux; Wonpil Im (Nucleic Acids Res., 2008)

Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms. - Sichun Yang; Benoît Roux (PLoS Comput. Biol., 2008)

CHARMM: The biomolecular simulation program. - Bernard R. Brooks; Charles L. Brooks III; Alexander D. MacKerell Jr.; Lennart Nilsson; Robert J. Petrella; Benoît Roux; Y. Won; G. Archontis; Christian Bartels; Stefan Boresch; Amedeo Caflisch; Leo S. D. Caves; et al. (J. Comput. Chem., 2009)

Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions. - Jean-François Truchon; Anthony Nicholls; J. Andrew Grant; Radu I. Iftimie; Benoît Roux; Christopher I. Bayly (J. Comput. Chem., 2010)

Membrane protein simulations under asymmetric ionic concentrations. - Fatemeh Khalili-Araghi; Brigitte Ziervogel; Benoît Roux; James C. Gumbart (XSEDE, 2012)

Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores. - Kyu Il Lee; Sunhwan Jo; Huan Rui; Bernhard Egwolf; Benoît Roux; Richard W. Pastor; Wonpil Im (J. Comput. Chem., 2012)

CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application. - Sunhwan Jo; Wei Jiang; Hui Sun Lee; Benoît Roux; Wonpil Im (J. Chem. Inf. Model., 2013)

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. - Wei Jiang; James C. Phillips; Lei Huang 019; Mikolai Fajer; Yilin Meng; James C. Gumbart; Yun Luo; Klaus Schulten; Benoît Roux (Comput. Phys. Commun., 2014)

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model. - Avisek Das; Mert Gur; Mary Hongying Cheng; Sunhwan Jo; Ivet Bahar; Benoît Roux (PLoS Comput. Biol., 2014)

Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations. - James C. Gumbart; Morgan Beeby; Grant J. Jensen; Benoît Roux (PLoS Comput. Biol., 2014)

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. - Justin A. Lemkul; Benoît Roux; David van der Spoel; Alexander D. MacKerell Jr. (J. Comput. Chem., 2015)

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments. - Rong Shen; Wei Han; Giacomo Fiorin; Shahidul M. Islam; Klaus Schulten; Benoît Roux (PLoS Comput. Biol., 2015)

CHARMM-GUI 10 years for biomolecular modeling and simulation. - Sunhwan Jo; Xi Cheng; Jumin Lee; Seonghoon Kim; Sang-Jun Park; Dhilon S. Patel; Andrew H. Beaven; Kyu Il Lee; Huan Rui; Soohyung Park; Hui Sun Lee; Benoît Roux; et al. (J. Comput. Chem., 2017)

Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model. - Alexey Aleksandrov; Fang-Yu Lin; Benoît Roux; Alexander D. MacKerell Jr. (J. Comput. Chem., 2018)

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. - Fang-Yu Lin; Pedro E. M. Lopes; Edward Harder; Benoît Roux; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2018)

Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD. - Wei Jiang; Christophe Chipot; Benoît Roux (J. Chem. Inf. Model., 2019)

Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols. - Ernest Awoonor-Williams; William C. Isley III; Stephen G. Dale; Erin R. Johnson; Haibo Yu 003; Axel D. Becke; Benoît Roux; Christopher N. Rowley (J. Comput. Chem., 2020)

CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations. - Yifei Qi; Jumin Lee; Xi Cheng; Rong Shen; Shahidul M. Islam; Benoît Roux; Wonpil Im (J. Comput. Chem., 2020)

Computational Modeling and Simulations of Biomolecular Systems - Benoît Roux (Computational Modeling and Simulations of Biomolecular Systems, 2021)

Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib. - Angela M. Barragan; Kyle Ghaby; Matthew P. Pond; Benoît Roux (J. Chem. Inf. Model., 2024)

Classifying Protein-Protein Binding Affinity with Free-Energy Calculations and Machine Learning Approaches. - Emma Goulard Coderc de Lacam; Benoît Roux; Christophe Chipot (J. Chem. Inf. Model., 2024)

Iterative variational learning of committor-consistent transition pathways using artificial neural networks. - Alberto Megías; Sergio Contreras Arredondo; Cheng Giuseppe Chen; Chenyu Tang; Benoît Roux; Christophe Chipot (Nat. Comput. Sci., 2025)