Benoı̂t Roux

Also affiliated with University of Chicago, Institute of Molecular Biology and Biotechnology

Biochemistry, Genetics and Molecular BiologyPhysics and AstronomyEngineering

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 49 papers. Top paper: “All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins”.

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

The Journal of Physical Chemistry B(1998)10.1021/jp973084f

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1.4DataRank · unranked

14461 citations

D. Bashford, M. Bellott, J. D. Evanseck, M. J. Field, S. Fischer +46 more

Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.0c00968

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0.568DataRank · unranked

43 citations

Hui Li, Alexander D. MacKerell, Toby W. Allen, Benoı̂t Roux, Sergei Y. Noskov +1 more

Open and Closed Structures of a Barium-Blocked Potassium Channel

Journal of Molecular Biology(2020)10.1016/j.jmb.2020.06.012

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0DataRank · unranked

24 citations

Lidong Gong, Jing Li, Huan Rui, Lydia Blachowicz, Benoı̂t Roux +1 more

Biochemical Patterns of Antibody Polyreactivity Revealed Through a Bioinformatics-Based Analysis of CDR Loops

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.30.229013

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0DataRank · unranked

5 citations

Marta T. Borowska, Jenna J. Guthmiller, Albert Bendelac, Patrick C. Wilson, Benoı̂t Roux +2 more

Barium blockade of the KcsA channel in open and closed conformation datasets

Data in Brief(2020)10.1016/j.dib.2020.106135

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0DataRank · unranked

2 citations

Lidong Gong, Jing Li, Huan Rui, Lydia Blachowicz, Benoı̂t Roux +1 more

String Method with Swarms-of-Trajectories, Mean Drifts, Lag Time, and Committor

The Journal of Physical Chemistry A(2021)10.1021/acs.jpca.1c04110

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0DataRank · unranked

47 citations

Benoı̂t Roux

Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.1c00664

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0DataRank · unranked

26 citations

Alexander D. MacKerell, Benoı̂t Roux, Chetan Rupakheti

Molecular Dynamics Simulations Based on Polarizable Models Show that Ion Permeation Interconverts between Different Mechanisms as a Function of Membrane Thickness

The Journal of Physical Chemistry B(2021)10.1021/acs.jpcb.0c08613

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0DataRank · unranked

25 citations

Igor Vorobyov, Benoı̂t Roux, Toby W. Allen, Peiran Chen

A critical perspective on Markov state model treatments of protein–protein association using coarse-grained simulations

The Journal of Chemical Physics(2021)10.1063/5.0039144

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0DataRank · unranked

22 citations

Fabian Paul, Benoı̂t Roux, Ziwei He

Computational study of non-conductive selectivity filter conformations and C-type inactivation in a voltage-dependent potassium channel

The Journal of General Physiology(2021)10.1085/jgp.202112875

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0DataRank · unranked

24 citations

Rong Shen, Ahmed Rohaim, Ramon Mendoza Uriarte, Mikolai Fajer, Eduardo Perozo +2 more

Tyrosine kinases: complex molecular systems challenging computational methodologies

The European Physical Journal B(2021)10.1140/epjb/s10051-021-00207-7

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0DataRank · unranked

13 citations

Benoı̂t Roux, Trayder Thomas

Folding and misfolding of potassium channel monomers during assembly and tetramerization

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2103674118

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0DataRank · unranked

6 citations

Andrew V. Molina, Ruofan Chen, Isabelle A. Gagnon, Young Hoon Koh, Benoı̂t Roux +2 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.22.461404

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0DataRank · unranked

1 citations

Bram J. A. Vermeulen, Jing Li, Felix Kümmerer, Federico Napoli, Lydia Blachowicz +4 more

Metal-Responsive Regulation of Enzyme Catalysis using Genetically Encoded Chemical Switches

RePEc: Research Papers in Economics(2021)10.33774/chemrxiv-2021-9ql74

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0DataRank · unranked

0 citations

Kosuke Seki, Ying Li, Andrew C. Hunt, Bingqing Liu, Benoı̂t Roux +3 more

Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations

Nature Protocols(2022)10.1038/s41596-021-00676-1

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0DataRank · unranked

176 citations

Haochuan Chen, Marharyta Blazhynska, Emma Goulard Coderc de Lacam, Florence Szczepaniak, Ànna Pavlova +7 more

Computational methods and theory for ion channel research

Advances in Physics X(2022)10.1080/23746149.2022.2080587

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0DataRank · unranked

34 citations

Fabio Cecconi, Letizia Chiodo, Grazia Cottone, Paolo Malgaretti, Luca Maragliano +8 more

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

Nature Communications(2022)10.1038/s41467-022-29239-y

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0DataRank · unranked

35 citations

Kosuke Seki, Ying Li, Andrew C. Hunt, Bingqing Liu, Benoı̂t Roux +3 more

Mechanism of voltage gating in the voltage-sensing phosphatase Ci-VSP

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2206649119

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0DataRank · unranked

23 citations

Yilin Meng, Benoı̂t Roux, Eduardo Perozo, Rong Shen

Galvani Offset Potential and Constant-pH Simulations of Membrane Proteins

The Journal of Physical Chemistry B(2022)10.1021/acs.jpcb.2c04593

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0DataRank · unranked

21 citations

Christophe Chipot, Stephan Kellenberger, Benoı̂t Roux, Olivier Bignucolo

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

Nature Communications(2022)10.1038/s41467-022-28866-9

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0DataRank · unranked

19 citations

Bram J. A. Vermeulen, Jing Li, Felix Kümmerer, Federico Napoli, Lydia Blachowicz +4 more

Engineering of a synthetic antibody fragment for structural and functional studies of K+ channels

The Journal of General Physiology(2022)10.1085/jgp.202112965

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0DataRank · unranked

3 citations

Tomasz Ślężak, Young Hoon Koh, Lydia Blachowicz, Anthony A. Kossiakoff, Benoı̂t Roux +1 more

Crystal Structure and Conformational Dynamics of Pyrococcus furio- sus Prolyl Oligopeptidase

ChemRxiv(2022)10.26434/chemrxiv-2022-878t5-v2

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0DataRank · unranked

6 citations

Huan Rui, Ryan Beckner, Poonam Srivastava, N. Sukumar, Benoı̂t Roux +2 more

Mechanism of Voltage Gating in the Voltage-Sensing Phosphatase Ci-VSP

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.17.480971

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0DataRank · unranked

3 citations

Yilin Meng, Benoı̂t Roux, Eduardo Perozo, Rong Shen

State Dependent Anionic Pore Currents Conducted by Single Countercharge Mutants in a Voltage-Sensing Phosphatase

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.04.487073

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0DataRank · unranked

1 citations

Benoı̂t Roux, Eduardo Perozo, Rong Shen

Dynamics of activation in the voltage-sensing domain of Ci-VSP

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.19.521128

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0DataRank · unranked

1 citations

Rong Shen, Benoı̂t Roux, Aaron R. Dinner, Spencer C. Guo

Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00203

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0DataRank · unranked

38 citations

Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor +4 more

A Rigorous Framework for Calculating Protein–Protein Binding Affinities in Membranes

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00941

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0DataRank · unranked

21 citations

James C. Gumbart, Haochuan Chen, Emad Tajkhorshid, Benoı̂t Roux, Christophe Chipot +1 more

Simulating the Voltage-Dependent Fluorescence of Di-8-ANEPPS in a Lipid Membrane

The Journal of Physical Chemistry Letters(2023)10.1021/acs.jpclett.3c01257

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0DataRank · unranked

12 citations

Benoı̂t Roux, Rachael Youngworth

Biochemical and biophysical characterization of natural polyreactivity in antibodies

Cell Reports(2023)10.1016/j.celrep.2023.113190

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0DataRank · unranked

15 citations

Christopher T. Boughter, Jeffrey J. Bunker, Jenna J. Guthmiller, Patrick C. Wilson, Benoı̂t Roux +3 more

Simulating the Fluorescence of the Locally Excited State of DMABN in Solvents of Different Polarities

The Journal of Physical Chemistry B(2023)10.1021/acs.jpcb.3c02975

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0DataRank · unranked

11 citations

Benoı̂t Roux, Rachael Youngworth

Anionic omega currents from single countercharge mutants in the voltage-sensing domain of Ci-VSP

The Journal of General Physiology(2023)10.1085/jgp.202213311

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0DataRank · unranked

5 citations

Benoı̂t Roux, Eduardo Perozo, Rong Shen

Simulating the Fluorescence of Di-8-ANEPPS in Solvents of Different Polarity

The Journal of Physical Chemistry B(2023)10.1021/acs.jpcb.3c02974

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0DataRank · unranked

7 citations

Benoı̂t Roux, Rachael Youngworth

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c04100

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0DataRank · unranked

116 citations

Steven L. Austin, Arnaud Blondel, Eric D. Boittier, Stefan Boresch, Matthias Buck +68 more

Dynamics of activation in the voltage-sensing domain of Ciona intestinalis phosphatase Ci-VSP

Nature Communications(2024)10.1038/s41467-024-45514-6

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0DataRank · unranked

16 citations

Rong Shen, Benoı̂t Roux, Aaron R. Dinner, Spencer C. Guo

How is Membrane Permeation of Small Ionizable Molecules Affected by Protonation Kinetics?

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.3c06765

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0DataRank · unranked

11 citations

Christophe Chipot, Benoı̂t Roux, Jonathan J. Harris

Computational Investigation of the Covalent Inhibition Mechanism of Bruton’s Tyrosine Kinase by Ibrutinib

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.4c00023

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0DataRank · unranked

10 citations

Kyle Ghaby, Matthew P. Pond, Benoı̂t Roux, Angela M. Barragan

Isoleucine gate blocks K+ conduction in C-type inactivation

eLife(2024)10.7554/elife.97696

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0DataRank · unranked

9 citations

Yichen Liu, Carlos A Z Bassetto, Bernardo I. Pinto, João Antonio Alves Nunes, Ramon Mendoza Uriarte +4 more

Statistical Mechanical Theories of Membrane Permeability

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c05020

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0DataRank · unranked

8 citations

Christophe Chipot, Benoı̂t Roux, Jonathan J. Harris

Configurational Sampling of All-Atom Solvated Membranes Using Hybrid Nonequilibrium Molecular Dynamics Monte Carlo Simulations

The Journal of Physical Chemistry Letters(2024)10.1021/acs.jpclett.4c00305

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0DataRank · unranked

5 citations

François Dehez, Benoı̂t Roux, Florence Szczepaniak

Probing the formation of a hetero-dimeric membrane transport complex with dual in vitro and in silico mutagenesis

Chemical Science(2024)10.1039/d4sc02915a

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0DataRank · unranked

1 citations

M. Joanne Lemieux, Christophe Chipot, Benoı̂t Roux, Howard S. Young, Nishadh Rathod

Hybrid neMD/MC lipid swapping algorithm to equilibrate membrane simulation with thermodynamic reservoir

The Journal of Chemical Physics(2024)10.1063/5.0230226

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0DataRank · unranked

1 citations

François Dehez, Benoı̂t Roux, Florence Szczepaniak

Isoleucine gate blocks K+ conduction in C-type inactivation

arXiv (Cornell University)(2024)10.48550/arxiv.2403.16179

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0DataRank · unranked

0 citations

Yichen Liu, Carlos A Z Bassetto, Bernardo I. Pinto, João Ferreira Alves, Christophe Chipot +3 more

Multistate Kinetic Model of the Sodium–Potassium ATPase

The Journal of Physical Chemistry B(2025)10.1021/acs.jpcb.5c04069

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0DataRank · unranked

5 citations

Huan Rui, Benoı̂t Roux, Jose Guerra

Force field sensitivity of ion occupancy in potassium channels

Biophysical Journal(2025)10.1016/j.bpj.2025.12.002

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0DataRank · unranked

1 citations

Benoı̂t Roux, Ramon Mendoza Uriarte

GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD

Journal of Chemical Information and Modeling(2025)10.1021/acs.jcim.5c02162

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0DataRank · unranked

1 citations

Christophe Chipot, Benoı̂t Roux, Sarah Moe

Conductance of a potassium channel in the limit of zero membrane potential

Biophysical Journal(2025)10.1016/j.bpj.2025.12.024

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0DataRank · unranked

1 citations

Benoı̂t Roux, Ramon Mendoza Uriarte

Kinetic Modeling of Covalent Inhibition: Effects of Rapidly Fluctuating Intermediate States

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.28.656658

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0DataRank · unranked

1 citations

Benoı̂t Roux, Kyle Ghaby

Molecular Dynamics-Guided Design and Chemoproteomic Profiling of Covalent Kinase Activity Probes

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.17.683178

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0DataRank · unranked

0 citations

Anthony J. Carlos, Trayder Thomas, Kyle Ghaby, Shaghayegh Fathi, Mukta Sharma +8 more

Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian

The Journal of Chemical Physics(2020)10.1063/5.0019987

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0DataRank · unranked

68 citations

Guillaume Lamoureux, Alexander D. MacKerell, Benoı̂t Roux, Chetan Rupakheti