Benoît Roux

Publication Activity (10 Years)

Years Active: 1995-2024
Publications (10 Years): 8

Top Topics

Protein Structural

Machine Learning Approaches

Graphical User Interface

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

PLoS Comput. Biol.

Comput. Phys. Commun.

Publications

Angela M. Barragan, Kyle Ghaby, Matthew P. Pond, Benoît Roux
Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib. J. Chem. Inf. Model. 64 (8) (2024)
Emma Goulard Coderc de Lacam, Benoît Roux, Christophe Chipot
Classifying Protein-Protein Binding Affinity with Free-Energy Calculations and Machine Learning Approaches. J. Chem. Inf. Model. 64 (3) (2024)
Ernest Awoonor-Williams, William C. Isley III, Stephen G. Dale, Erin R. Johnson, Haibo Yu, Axel D. Becke, Benoît Roux, Christopher N. Rowley
Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols. J. Comput. Chem. 41 (5) (2020)
Yifei Qi, Jumin Lee, Xi Cheng, Rong Shen, Shahidul M. Islam, Benoît Roux, Wonpil Im
CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations. J. Comput. Chem. 41 (5) (2020)
Wei Jiang, Christophe Chipot, Benoît Roux
Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD. J. Chem. Inf. Model. 59 (9) (2019)
Fang-Yu Lin, Pedro E. M. Lopes, Edward Harder, Benoît Roux, Alexander D. MacKerell Jr.
Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. J. Chem. Inf. Model. 58 (5) (2018)
Alexey Aleksandrov, Fang-Yu Lin, Benoît Roux, Alexander D. MacKerell Jr.
Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model. J. Comput. Chem. 39 (22) (2018)
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
CHARMM-GUI 10 years for biomolecular modeling and simulation. J. Comput. Chem. 38 (15) (2017)
Rong Shen, Wei Han, Giacomo Fiorin, Shahidul M. Islam, Klaus Schulten, Benoît Roux
Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments. PLoS Comput. Biol. 11 (10) (2015)
Justin A. Lemkul, Benoît Roux, David van der Spoel, Alexander D. MacKerell Jr.
Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. J. Comput. Chem. 36 (19) (2015)
James C. Gumbart, Morgan Beeby, Grant J. Jensen, Benoît Roux
Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations. PLoS Comput. Biol. 10 (2) (2014)
Avisek Das, Mert Gur, Mary Hongying Cheng, Sunhwan Jo, Ivet Bahar, Benoît Roux
Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model. PLoS Comput. Biol. 10 (4) (2014)
Wei Jiang, James C. Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James C. Gumbart, Yun Luo, Klaus Schulten, Benoît Roux
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. Comput. Phys. Commun. 185 (3) (2014)
Sunhwan Jo, Wei Jiang, Hui Sun Lee, Benoît Roux, Wonpil Im
CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application. J. Chem. Inf. Model. 53 (1) (2013)
Kyu Il Lee, Sunhwan Jo, Huan Rui, Bernhard Egwolf, Benoît Roux, Richard W. Pastor, Wonpil Im
Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores. J. Comput. Chem. 33 (3) (2012)
Fatemeh Khalili-Araghi, Brigitte Ziervogel, Benoît Roux, James C. Gumbart
Membrane protein simulations under asymmetric ionic concentrations. XSEDE (2012)
Jean-François Truchon, Anthony Nicholls, J. Andrew Grant, Radu I. Iftimie, Benoît Roux, Christopher I. Bayly
Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions. J. Comput. Chem. 31 (4) (2010)
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, V. 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
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30 (10) (2009)
Sichun Yang, Benoît Roux
Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms. PLoS Comput. Biol. 4 (3) (2008)
Sunhwan Jo, Miklós Vargyas, Judit Vasko-Szedlar, Benoît Roux, Wonpil Im
PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
José D. Faraldo-Gómez, Benoît Roux
Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects. J. Comput. Chem. 28 (10) (2007)
Serge Crouzy, Jérôme Baudry, Jeremy C. Smith, Benoît Roux
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. 20 (15) (1999)
Konrad Hinsen, Benoît Roux
A potential function for computer simulation studies of proton transfer in acetylacetone. J. Comput. Chem. 18 (3) (1997)
Jérôme Baudry, Serge Crouzy, Benoît Roux, Jeremy C. Smith
Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational Energetics. J. Chem. Inf. Comput. Sci. 37 (6) (1997)
Benoît Roux, Martin Karplus
Potential Energy Function for Cation-Peptide Interactions: An Ab Initio Study. J. Comput. Chem. 16 (6) (1995)