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2020 – today
- 2024
[j24]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): 1081-1091 (2024)- [j23]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): 3488-3502 (2024) - 2021
- [b1]Benoît Roux:
Computational Modeling and Simulations of Biomolecular Systems. WorldScientific 2021, ISBN 9789811232756, pp. 1-208 - 2020
- [j22]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): 415-420 (2020) - [j21]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): 427-438 (2020)
2010 – 2019
- 2019
- [j20]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): 3794-3802 (2019) - 2018
- [j19]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): 1707-1719 (2018) - [j18]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): 993-1004 (2018) - 2017
- [j17]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): 1114-1124 (2017) - 2015
- [j16]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): 1473-1479 (2015) - [j15]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) - 2014
- [j14]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): 908-916 (2014) - [j13]James C. Gumbart, Morgan Beeby, Grant J. Jensen, Benoît Roux:
Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations. PLoS Comput. Biol. 10(2) (2014) - [j12]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) - 2013
- [j11]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): 267-277 (2013) - 2012
- [j10]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): 331-339 (2012) - [c1]Fatemeh Khalili-Araghi, Brigitte Ziervogel, Benoît Roux, James C. Gumbart:
Membrane protein simulations under asymmetric ionic concentrations. XSEDE 2012: 16:1 - 2010
- [j9]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): 811-824 (2010)
2000 – 2009
- 2009
- [j8]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:
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30(10): 1545-1614 (2009) - 2008
- [j7]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): 270-275 (2008) - [j6]Sichun Yang, Benoît Roux:
Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms. PLoS Comput. Biol. 4(3) (2008) - 2007
- [j5]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): 1634-1647 (2007)
1990 – 1999
- 1999
- [j4]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): 1644-1658 (1999) - [p1]Ron Elber, Benoît Roux, Roberto Olender:
Application of a Stochastic Path Integral Approach to the Computations of an Optimal Path and Ensembles of Trajectories. Computational Molecular Dynamics 1999: 263-280 - 1997
- [j3]Konrad Hinsen, Benoît Roux:
A potential function for computer simulation studies of proton transfer in acetylacetone. J. Comput. Chem. 18(3): 368-380 (1997) - [j2]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): 1018-1024 (1997) - 1995
- [j1]Benoît Roux, Martin Karplus:
Potential Energy Function for Cation-Peptide Interactions: An Ab Initio Study. J. Comput. Chem. 16(6): 690-704 (1995)
Coauthor Index
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