Benoît Roux - researchr alias

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Viewing Publication 1 - 23 from 23

2024

Classifying Protein-Protein Binding Affinity with Free-Energy Calculations and Machine Learning ApproachesEmma Goulard Coderc de Lacam, Benoît Roux, Christophe Chipot. jcisd, 64(3):1081-1091, 2024. [doi]

2021

Computational Modeling and Simulations of Biomolecular SystemsBenoît Roux. WorldScientific, 2021. [doi]

2020

2019

Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMDWei Jiang, Christophe Chipot, Benoît Roux. jcisd, 59(9):3794-3802, 2019. [doi]

2018

Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation modelAlexey Aleksandrov, Fang-Yu Lin, Benoît Roux, Alexander D. MacKerell Jr.. jcc, 39(22):1707-1719, 2018. [doi]

Polarizable Force Field for Molecular Ions Based on the Classical Drude OscillatorFang-Yu Lin, Pedro E. M. Lopes, Edward Harder, Benoît Roux, Alexander D. MacKerell Jr.. jcisd, 58(5):993-1004, 2018. [doi]

2017

CHARMM-GUI 10 years for biomolecular modeling and simulationSunhwan 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. jcc, 38(15):1114-1124, 2017. [doi]

2015

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator modelJustin A. Lemkul, Benoît Roux, David van der Spoel, Alexander D. MacKerell Jr.. jcc, 36(19):1473-1479, 2015. [doi]

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular FragmentsRong Shen, Wei Han, Giacomo Fiorin, Shahidul M. Islam, Klaus Schulten, Benoît Roux. ploscb, 11(10), 2015. [doi]

2014

2013

CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its ApplicationSunhwan Jo, Wei Jiang, Hui Sun Lee, Benoît Roux, Wonpil Im. jcisd, 53(1):267-277, 2013. [doi]

2012

Membrane protein simulations under asymmetric ionic concentrationsFatemeh Khalili-Araghi, Brigitte Ziervogel, Benoît Roux, James C. Gumbart. xsede 2012: [doi]

Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel poresKyu-Il Lee, Sunhwan Jo, Huan Rui, Bernhard Egwolf, Benoît Roux, Richard W. Pastor, Wonpil Im. jcc, 33(3):331-339, 2012. [doi]

2008

Src Kinase Conformational Activation: Thermodynamics, Pathways, and MechanismsSichun Yang, Benoît Roux. ploscb, 4(3), 2008. [doi]

2007

Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effectsJosé D. Faraldo-Gómez, Benoît Roux. jcc, 28(10):1634-1647, 2007. [doi]

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 bacteriorhodopsinSerge Crouzy, Jérôme Baudry, Jeremy C. Smith, Benoît Roux. jcc, 20(15):1644-1658, 1999. [doi]

Application of a Stochastic Path Integral Approach to the Computations of an Optimal Path and Ensembles of TrajectoriesRon Elber, Benoît Roux, Roberto Olender. In Peter Deuflhard, Jan Hermans, Benedict J. Leimkuhler, Alan E. Mark, Sebastian Reich, Robert D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas. Volume 4 of Lecture Notes in Computational Science and Engineering, pages 263-280, Springer, 1999. [doi]

1997

Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational EnergeticsJérôme Baudry, Serge Crouzy, Benoît Roux, Jeremy C. Smith. jcisd, 37(6):1018-1024, 1997. [doi]

A potential function for computer simulation studies of proton transfer in acetylacetoneKonrad Hinsen, Benoît Roux. jcc, 18(3):368-380, 1997. [doi]

1995

Potential Energy Function for Cation-Peptide Interactions: An Ab Initio StudyBenoît Roux, Martin Karplus. jcc, 16(6):690-704, 1995.

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