Works by Roux, Benoît

Results: 75

Conformational dynamics of ligand-dependent alternating access in LeuT.

Published in:

Nature Structural & Molecular Biology, 2014, v. 21, n. 5, p. 472, doi. 10.1038/nsmb.2816

By:

Kazmier, Kelli;
Sharma, Shruti;
Quick, Matthias;
Islam, Shahidul M;
Roux, Benoît;
Weinstein, Harel;
Javitch, Jonathan A;
Mchaourab, Hassane S

Publication type:

Article

Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain.

Published in:

Nature Structural & Molecular Biology, 2014, v. 21, n. 3, p. 244, doi. 10.1038/nsmb.2768

By:

Li, Qufei;
Wanderling, Sherry;
Paduch, Marcin;
Medovoy, David;
Singharoy, Abhishek;
McGreevy, Ryan;
Villalba-Galea, Carlos A;
Hulse, Raymond E;
Roux, Benoît;
Schulten, Klaus;
Kossiakoff, Anthony;
Perozo, Eduardo

Publication type:

Article

Protonation of key acidic residues is critical for the K+-selectivity of the Na/K pump.

Published in:

Nature Structural & Molecular Biology, 2011, v. 18, n. 10, p. 1159, doi. 10.1038/nsmb.2113

By:

Yu, Haibo;
Ratheal, Ian M;
Artigas, Pablo;
Roux, Benoît

Publication type:

Article

The hidden energetics of ligand binding and activation in a glutamate receptor.

Published in:

Nature Structural & Molecular Biology, 2011, v. 18, n. 3, p. 283, doi. 10.1038/nsmb.2010

By:

Lau, Albert Y.;
Roux, Benoît

Publication type:

Article

On the structural basis of modal gating behavior in K+ channels.

Published in:

Nature Structural & Molecular Biology, 2011, v. 18, n. 1, p. 67, doi. 10.1038/nsmb.1968

By:

Chakrapani, Sudha;
Cordero-Morales, Julio F;
Jogini, Vishwanath;
Pan, Albert C;
Cortes, D Marien;
Roux, Benoît;
Perozo, Eduardo

Publication type:

Article

Molecular driving forces determining potassium channel slow inactivation.

Published in:

Nature Structural & Molecular Biology, 2007, v. 14, n. 11, p. 1062, doi. 10.1038/nsmb1309

By:

Cordero-Morales, Julio F.;
Jogini, Vishwanath;
Lewis, Anthony;
Vásquez, Valeria;
Cortes, D. Marien;
Roux, Benoît;
Perozo, Eduardo

Publication type:

Article

Molecular determinants of gating at the potassium-channel selectivity filter.

Published in:

Nature Structural & Molecular Biology, 2006, v. 13, n. 4, p. 311, doi. 10.1038/nsmb1069

By:

Cordero-Morales, Julio F;
Cuello, Luis G;
Zhao, Yanxiang;
Jogini, Vishwanath;
Cortes, D Marien;
Roux, Benoît;
Perozo, Eduardo

Publication type:

Article

1H, 15N, and 13C resonance assignments of the intrinsically disordered SH4 and Unique domains of Hck.

Published in:

Biomolecular NMR Assignments, 2019, v. 13, n. 1, p. 71, doi. 10.1007/s12104-018-9854-z

By:

Pond, Matthew P.;
Blachowicz, Lydia;
Roux, Benoît

Publication type:

Article

Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects.

Published in:

Journal of Computational Chemistry, 2007, v. 28, n. 10, p. 1634, doi. 10.1002/jcc.20652

By:

Faraldo-Gómez, José D.;
Roux, Benoît

Publication type:

Article

Efficient calculation of two-dimensional adiabatic and free energy maps: Application to the isomerization of the C13C14 and C15N16 bonds in the retinal of bacteriorhodopsin.

Published in:

Journal of Computational Chemistry, 1999, v. 20, n. 15, p. 1644, doi. 10.1002/(SICI)1096-987X(19991130)20:15<1644::AID-JCC5>3.0.CO;2-Y

By:

Crouzy, Serge;
Baudry, Jerôme;
Smith, Jeremy C.;
Roux, Benoît

Publication type:

Article

Mixing quantum-classical molecular dynamics methods applied to intramolecular proton transfer in acetylacetone.

Published in:

Journal of Computational Chemistry, 1997, v. 18, n. 14, p. 1760, doi. 10.1002/(SICI)1096-987X(19971115)18:14<1760::AID-JCC5>3.0.CO;2-I

By:

Sharafeddin, Omar A.;
Hinsen, Konrad;
Carrington, Tucker;
Roux, Benoît

Publication type:

Article

A potential function for computer simulation studies of proton transfer in acetylacetone.

Published in:

Journal of Computational Chemistry, 1997, v. 18, n. 3, p. 368, doi. 10.1002/(SICI)1096-987X(199702)18:3<368::AID-JCC7>3.0.CO;2-S

By:

Hinsen, Konrad;
Roux, Benoît

Publication type:

Article

Potential energy function for cation-peptide interactions: An ab initio study.

Published in:

Journal of Computational Chemistry, 1995, v. 16, n. 6, p. 690, doi. 10.1002/jcc.540160605

By:

Roux, Benoît;
Karplus, Martin

Publication type:

Article

Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-29239-y

By:

Zubi, Yasmine S.;
Seki, Kosuke;
Li, Ying;
Hunt, Andrew C.;
Liu, Bingqing;
Roux, Benoît;
Jewett, Michael C.;
Lewis, Jared C.

Publication type:

Article

A distinct mechanism of C-type inactivation in the Kv-like KcsA mutant E71V.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28866-9

By:

Rohaim, Ahmed;
Vermeulen, Bram J. A.;
Li, Jing;
Kümmerer, Felix;
Napoli, Federico;
Blachowicz, Lydia;
Medeiros-Silva, João;
Roux, Benoît;
Weingarth, Markus

Publication type:

Article

The emergence of protein dynamics simulations: how computational statistical mechanics met biochemistry.

Published in:

European Physical Journal H, 2022, v. 47, n. 1, p. 1, doi. 10.1140/epjh/s13129-022-00043-y

By:

Macuglia, Daniele;
Roux, Benoît;
Ciccotti, Giovanni

Publication type:

Article

The breakthrough of a quantum chemist by classical dynamics: Martin Karplus and the birth of computer simulations of chemical reactions.

Published in:

European Physical Journal H, 2021, v. 46, n. 1, p. 1, doi. 10.1140/epjh/s13129-021-00013-w

By:

Macuglia, Daniele;
Roux, Benoît;
Ciccotti, Giovanni

Publication type:

Article

Architecture and assembly of the Gram-positive cell wall.

Published in:

Molecular Microbiology, 2013, v. 88, n. 4, p. 664, doi. 10.1111/mmi.12203

By:

Beeby, Morgan;
Gumbart, James C.;
Roux, Benoît;
Jensen, Grant J.

Publication type:

Article

Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms.

Published in:

PLoS Computational Biology, 2008, v. 4, n. 3, p. 1, doi. 10.1371/journal.pcbi.1000047

By:

Sichun Yang;
Roux, Benoît

Publication type:

Article

Bulletin de la Société Paul Claudel. 2023 - 2, n° 240 - Deux Annonce faite à Marie: un opéra et un film restauré.

Published in:

2023

By:

Chevalier, Jean-Frédéric;
Danguy, Laurence;
Roux, Benoît Le;
Nantet, Marie-Victoire

Publication type:

Book Review

Shifts in the selectivity filter dynamics cause modal gating in K+ channels.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-018-07973-6

By:

Jekhmane, Shehrazade;
Medeiros-Silva, João;
Jing Li;
Kümmerer, Felix;
Müller-Hermes, Christoph;
Baldus, Marc;
Roux, Benoît;
Weingarth, Markus

Publication type:

Article

Molecular Mechanisms of K[+] Selectivity in Na/K Pump.

Published in:

Australian Journal of Chemistry, 2012, v. 65, n. 5, p. 8

By:

YuHaibo;
Ratheal, Ian;
Artigas, Pablo;
Roux, Benoît

Publication type:

Article

Critical assessment of a proposed model of Shaker

Published in:

FEBS Letters, 2004, v. 564, n. 3, p. 257, doi. 10.1016/S0014-5793(04)00273-X

By:

Lainé, Muriel;
Papazian, Diane M.;
Roux, Benoît

Publication type:

Article

Binding specificity of SH2 domains: Insight from free energy simulations.

Published in:

Proteins, 2009, v. 74, n. 4, p. 996, doi. 10.1002/prot.22209

By:

Gan, Wenxun;
Roux, Benoît

Publication type:

Article

Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases.

Published in:

Proteins, 2009, v. 74, n. 2, p. 378, doi. 10.1002/prot.22153

By:

Banavali, Nilesh K.;
Roux, Benoît

Publication type:

Article

Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck.

Published in:

Proteins, 2007, v. 67, n. 4, p. 1096, doi. 10.1002/prot.21334

By:

Banavali, Nilesh K.;
Roux, Benoît

Publication type:

Article

Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer.

Published in:

Proteins, 1996, v. 24, n. 1, p. 92, doi. 10.1002/(SICI)1097-0134(199601)24:1<92::AID-PROT7>3.0.CO;2-Q

By:

Woolf, Thomas B.;
Roux, Benoît

Publication type:

Article

Concepts and protocols for electrostatic free energies.

Published in:

Molecular Simulation, 2016, v. 42, n. 13, p. 1090, doi. 10.1080/08927022.2015.1121544

By:

Simonson, Thomas;
Roux, Benoît

Publication type:

Article

Achieving ergodic sampling using replica-exchange free-energy calculations.

Published in:

Molecular Simulation, 2014, v. 40, n. 1-3, p. 218, doi. 10.1080/08927022.2013.841909

By:

Comer, Jeffrey;
Roux, Benoît;
Chipot, Christophe

Publication type:

Article

Crystal structure of an archaeal CorB magnesium transporter.

Published in:

Nature Communications, 2021, v. 12, p. 1, doi. 10.1038/s41467-021-24282-7

By:

Chen, Yu Seby;
Kozlov, Guennadi;
Moeller, Brandon E.;
Rohaim, Ahmed;
Fakih, Rayan;
Roux, Benoît;
Burke, John E.;
Gehring, Kalle

Publication type:

Article

Theoretical and computational models of biological ion channels.

Published in:

Quarterly Reviews of Biophysics, 2004, v. 37, n. 1, p. 15, doi. 10.1017/S0033583504003968

By:

Roux, Benoît;
Allen, Toby;
Bernèche, Simon;
Im, Wonpil

Publication type:

Article

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 10, p. 1, doi. 10.1371/journal.pcbi.1004368

By:

Shen, Rong;
Han, Wei;
Fiorin, Giacomo;
Islam, Shahidul M.;
Schulten, Klaus;
Roux, Benoît

Publication type:

Article

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 4, p. 1, doi. 10.1371/journal.pcbi.1003521

By:

Das, Avisek;
Gur, Mert;
Cheng, Mary Hongying;
Jo, Sunhwan;
Bahar, Ivet;
Roux, Benoît

Publication type:

Article

Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 2, p. 1, doi. 10.1371/journal.pcbi.1003475

By:

Gumbart, James C.;
Beeby, Morgan;
Jensen, Grant J.;
Roux, Benoît

Publication type:

Article

Tyrosine kinases: complex molecular systems challenging computational methodologies.

Published in:

European Physical Journal B: Condensed Matter, 2021, v. 94, n. 10, p. 1, doi. 10.1140/epjb/s10051-021-00207-7

By:

Thomas, Trayder;
Roux, Benoît

Publication type:

Article

Combining the polarizable Drude force field with a continuum electrostatic Poisson–Boltzmann implicit solvation model.

Published in:

Journal of Computational Chemistry, 2018, v. 39, n. 22, p. 1707, doi. 10.1002/jcc.25345

By:

Aleksandrov, Alexey;
Lin, Fang‐Yu;
MacKerell, Jr., Alexander D.;
Roux, Benoît

Publication type:

Article

CHARMM-GUI 10 years for biomolecular modeling and simulation.

Published in:

Journal of Computational Chemistry, 2017, v. 38, n. 15, p. 1114, doi. 10.1002/jcc.24660

By:

Jo, Sunhwan;
Cheng, Xi;
Lee, Jumin;
Kim, Seonghoon;
Park, Sang‐Jun;
Patel, Dhilon S.;
Beaven, Andrew H.;
Lee, Kyu Il;
Rui, Huan;
Park, Soohyung;
Lee, Hui Sun;
Roux, Benoît;
MacKerell, Alexander D.;
Klauda, Jeffrey B.;
Qi, Yifei;
Im, Wonpil

Publication type:

Article

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

Published in:

Journal of Computational Chemistry, 2015, v. 36, n. 19, p. 1473, doi. 10.1002/jcc.23937

By:

Lemkul, Justin A.;
Roux, Benoît;
van der Spoel, David;
MacKerell, Alexander D.

Publication type:

Article

Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores.

Published in:

Journal of Computational Chemistry, 2012, v. 33, n. 3, p. 331, doi. 10.1002/jcc.21952

By:

Lee, Kyu Il;
Jo, Sunhwan;
Rui, Huan;
Egwolf, Bernhard;
Roux, Benoît;
Pastor, Richard W.;
Im, Wonpil

Publication type:

Article

Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions.

Published in:

Journal of Computational Chemistry, 2010, v. 31, n. 4, p. 811, doi. 10.1002/jcc.21369

By:

TRUCHON, JEAN-FRANÇOIS;
NICHOLL'S, ANTHONY;
GRANT, J. ANDREW;
IFTIMIE, RADU I.;
ROUX, BENOÎT;
BAYLY, CHRISTOPHER I.

Publication type:

Article

Dominant solvation effects from the primary shell of hydration: Approximation for molecular dynamics simulations.

Published in:

Biopolymers, 1995, v. 35, n. 2, p. 171, doi. 10.1002/bip.360350205

By:

Beglov, Dmitrii;
Roux, Benoît

Publication type:

Article

Anchoring of a monotopic membrane protein: the binding of prostaglandin H[sub 2] synthase-1 to the surface of a phospholipid bilayer.

Published in:

European Biophysics Journal, 2000, v. 29, n. 6, p. 439, doi. 10.1007/PL00006649

By:

Nina, Mafalda;
Bernèche, Simon;
Roux, Benoît

Publication type:

Article

Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola.

Published in:

Nature Communications, 2016, v. 7, n. 9, p. 12753, doi. 10.1038/ncomms12753

By:

Dhakshnamoorthy, Balasundaresan;
Rohaim, Ahmed;
Rui, Huan;
Blachowicz, Lydia;
Roux, Benoît

Publication type:

Article

Mechanism of potassium ion uptake by the Na+/K+-ATPase.

Published in:

Nature Communications, 2015, v. 6, n. 7, p. 7622, doi. 10.1038/ncomms8622

By:

Castillo, Juan P.;
Rui, Huan;
Basilio, Daniel;
Das, Avisek;
Roux, Benoît;
Latorre, Ramon;
Bezanilla, Francisco;
Holmgren, Miguel

Publication type:

Article

Activation pathway of Src kinase reveals intermediate states as targets for drug design.

Published in:

Nature Communications, 2014, v. 5, n. 3, p. 3397, doi. 10.1038/ncomms4397

By:

Shukla, Diwakar;
Meng, Yilin;
Roux, Benoît;
Pande, Vijay S.

Publication type:

Article

Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols.

Published in:

Journal of Computational Chemistry, 2020, v. 41, n. 5, p. 427, doi. 10.1002/jcc.26064

By:

Awoonor‐Williams, Ernest;
Isley, William C.;
Dale, Stephen G.;
Johnson, Erin R.;
Yu, Haibo;
Becke, Axel D.;
Roux, Benoît;
Rowley, Christopher N.

Publication type:

Article

CHARMM‐GUI DEER facilitator for spin‐pair distance distribution calculations and preparation of restrained‐ensemble molecular dynamics simulations.

Published in:

Journal of Computational Chemistry, 2020, v. 41, n. 5, p. 415, doi. 10.1002/jcc.26032

By:

Qi, Yifei;
Lee, Jumin;
Cheng, Xi;
Shen, Rong;
Islam, Shahidul M.;
Roux, Benoît;
Im, Wonpil

Publication type:

Article

Structural biology: One domain, multiple conformations.

Published in:

Nature Chemical Biology, 2011, v. 7, n. 3, p. 130, doi. 10.1038/nchembio.527

By:

Lau, Albert Y.;
Roux, Benoît

Publication type:

Article

A proton-controlled check valve for sodium ion transport.

Published in:

2007

By:

Roux, Benoît

Publication type:

Editorial

Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement.

Published in:

Nature, 2005, v. 436, n. 7052, p. 852, doi. 10.1038/nature03888

By:

Chanda, Baron;
Asamoah, Osei Kwame;
Blunck, Rikard;
Roux, Benoît;
Bezanilla, Francisco

Publication type:

Article