Benoît Roux

29 papers Journal 26Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD.
J. Chem. Inf. Model.
Sarah Moe, Christophe Chipot, Benoît Roux
2025 J jnl
Iterative variational learning of committor-consistent transition pathways using artificial neural networks.
Nat. Comput. Sci.
Alberto Megías, Sergio Contreras Arredondo, Cheng Giuseppe Chen, Chenyu Tang, Benoît Roux, Christophe Chipot
2025 J jnl
Kinetic Modeling of Covalent Inhibition: Effects of Rapidly Fluctuating Intermediate States.
J. Chem. Inf. Model.
Kyle Ghaby, Benoît Roux
2024 J jnl
Classifying Protein-Protein Binding Affinity with Free-Energy Calculations and Machine Learning Approaches.
J. Chem. Inf. Model.
Emma Goulard Coderc de Lacam, Benoît Roux, Christophe Chipot
2024 J jnl
Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib.
J. Chem. Inf. Model.
Angela M. Barragan, Kyle Ghaby, Matthew P. Pond, Benoît Roux
2021 — book
Computational Modeling and Simulations of Biomolecular Systems
Computational Modeling and Simulations of Biomolecular Systems
Benoît Roux
2020 J jnl
CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations.
J. Comput. Chem.
Yifei Qi, Jumin Lee, Xi Cheng, Rong Shen, Shahidul M. Islam, Benoît Roux, Wonpil Im
2020 J jnl
Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols.
J. Comput. Chem.
Ernest Awoonor-Williams, William C. Isley III, Stephen G. Dale, Erin R. Johnson, Haibo Yu, Axel D. Becke, Benoît Roux, Christopher N. Rowley
2019 J jnl
Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD.
J. Chem. Inf. Model.
Wei Jiang, Christophe Chipot, Benoît Roux
2018 J jnl
Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.
J. Comput. Chem.
Alexey Aleksandrov, Fang-Yu Lin, Benoît Roux, Alexander D. MacKerell Jr.
2018 J jnl
Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.
J. Chem. Inf. Model.
Fang-Yu Lin, Pedro E. M. Lopes, Edward Harder, Benoît Roux, Alexander D. MacKerell Jr.
2017 J jnl
CHARMM-GUI 10 years for biomolecular modeling and simulation.
J. Comput. Chem.
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, Alexander D. MacKerell Jr., Jeffrey B. Klauda, Yifei Qi, Wonpil Im
2015 J jnl
Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.
J. Comput. Chem.
Justin A. Lemkul, Benoît Roux, David van der Spoel, Alexander D. MacKerell Jr.
2015 J jnl
Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.
PLoS Comput. Biol.
Rong Shen, Wei Han, Giacomo Fiorin, Shahidul M. Islam, Klaus Schulten, Benoît Roux
2014 J jnl
Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model.
PLoS Comput. Biol.
Avisek Das, Mert Gur, Mary Hongying Cheng, Sunhwan Jo, Ivet Bahar, Benoît Roux
2014 J jnl
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD.
Comput. Phys. Commun.
Wei Jiang, James C. Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James C. Gumbart, Yun Luo, Klaus Schulten, Benoît Roux
2013 J jnl
CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application.
J. Chem. Inf. Model.
Sunhwan Jo, Wei Jiang, Hui Sun Lee, Benoît Roux, Wonpil Im
2012 — conf
Membrane protein simulations under asymmetric ionic concentrations.
XSEDE
Fatemeh Khalili-Araghi, Brigitte Ziervogel, Benoît Roux, James C. Gumbart
2012 J jnl
Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores.
J. Comput. Chem.
Kyu Il Lee, Sunhwan Jo, Huan Rui, Bernhard Egwolf, Benoît Roux, Richard W. Pastor, Wonpil Im
2010 J jnl
Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions.
J. Comput. Chem.
Jean-François Truchon, Anthony Nicholls, J. Andrew Grant, Radu I. Iftimie, Benoît Roux, Christopher I. Bayly
2009 J jnl
CHARMM: The biomolecular simulation program.
J. Comput. Chem.
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, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, Victor Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus
2008 J jnl
PBEQ-Solver for online visualization of electrostatic potential of biomolecules.
Nucleic Acids Res.
Sunhwan Jo, Miklós Vargyas, Judit Vasko-Szedlar, Benoît Roux, Wonpil Im
2008 J jnl
Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms.
PLoS Comput. Biol.
Sichun Yang, Benoît Roux
2007 J jnl
Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects.
J. Comput. Chem.
José D. Faraldo-Gómez, Benoît Roux
1999 — ch.
Application of a Stochastic Path Integral Approach to the Computations of an Optimal Path and Ensembles of Trajectories.
Computational Molecular Dynamics
Ron Elber, Benoît Roux, Roberto Olender
1999 J jnl
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.
J. Comput. Chem.
Serge Crouzy, Jérôme Baudry, Jeremy C. Smith, Benoît Roux
1997 J jnl
A potential function for computer simulation studies of proton transfer in acetylacetone.
J. Comput. Chem.
Konrad Hinsen, Benoît Roux
1997 J jnl
Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational Energetics.
J. Chem. Inf. Comput. Sci.
Jérôme Baudry, Serge Crouzy, Benoît Roux, Jeremy C. Smith
1995 J jnl
Potential Energy Function for Cation-Peptide Interactions: An Ab Initio Study.
J. Comput. Chem.
Benoît Roux, Martin Karplus