PubRank

Benoît Roux

Author PubWeight™ 199.03‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Molecular determinants of gating at the potassium-channel selectivity filter. Nat Struct Mol Biol 2006 4.64
2 Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 2004 4.37
3 Closing in on the resting state of the Shaker K(+) channel. Neuron 2007 3.49
4 Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci U S A 2005 3.21
5 Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement. Nature 2005 2.98
6 Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys J 2006 2.88
7 Two atomic constraints unambiguously position the S4 segment relative to S1 and S2 segments in the closed state of Shaker K channel. Proc Natl Acad Sci U S A 2007 2.85
8 Computations of standard binding free energies with molecular dynamics simulations. J Phys Chem B 2009 2.80
9 Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels. J Gen Physiol 2007 2.79
10 Energetics of ion conduction through the gramicidin channel. Proc Natl Acad Sci U S A 2003 2.67
11 Structural basis for the coupling between activation and inactivation gates in K(+) channels. Nature 2010 2.63
12 Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory. J Mol Biol 2002 2.61
13 Molecular driving forces determining potassium channel slow inactivation. Nat Struct Mol Biol 2007 2.56
14 A gate in the selectivity filter of potassium channels. Structure 2005 2.50
15 The free energy landscapes governing conformational changes in a glutamate receptor ligand-binding domain. Structure 2007 2.45
16 Ion selectivity in potassium channels. Biophys Chem 2006 2.28
17 Control of ion selectivity in LeuT: two Na+ binding sites with two different mechanisms. J Mol Biol 2008 2.27
18 A microscopic view of ion conduction through the K+ channel. Proc Natl Acad Sci U S A 2003 2.24
19 Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution. J Mol Biol 2002 2.23
20 Finding transition pathways using the string method with swarms of trajectories. J Phys Chem B 2008 2.17
21 Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field. J Phys Chem B 2006 2.15
22 The hidden energetics of ligand binding and activation in a glutamate receptor. Nat Struct Mol Biol 2011 2.10
23 Dynamics of the Kv1.2 voltage-gated K+ channel in a membrane environment. Biophys J 2007 2.10
24 Modeling the structure of agitoxin in complex with the Shaker K+ channel: a computational approach based on experimental distance restraints extracted from thermodynamic mutant cycles. Biophys J 2002 1.98
25 Molecular mechanism of H+ conduction in the single-file water chain of the gramicidin channel. Biophys J 2002 1.94
26 Ion permeation through the alpha-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory. Biophys J 2004 1.91
27 Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Biophys J 2010 1.87
28 Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput 2007 1.86
29 Multidomain assembled states of Hck tyrosine kinase in solution. Proc Natl Acad Sci U S A 2010 1.79
30 Polarizable empirical force field for aromatic compounds based on the classical drude oscillator. J Phys Chem B 2007 1.77
31 An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations. J Gen Physiol 2012 1.72
32 Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Proc Natl Acad Sci U S A 2009 1.70
33 Force field bias in protein folding simulations. Biophys J 2009 1.67
34 Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations. J Chem Phys 2008 1.66
35 A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes. Biophys J 2009 1.63
36 PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res 2008 1.61
37 Structural basis of two-stage voltage-dependent activation in K+ channels. Proc Natl Acad Sci U S A 2003 1.61
38 Electrostatics of ion stabilization in a ClC chloride channel homologue from Escherichia coli. J Mol Biol 2004 1.61
39 Understanding the dielectric properties of liquid amides from a polarizable force field. J Phys Chem B 2008 1.57
40 The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation. Structure 2005 1.53
41 Molecular basis of proton blockage in aquaporins. Structure 2004 1.51
42 Electrostatics of the intracellular vestibule of K+ channels. J Mol Biol 2005 1.48
43 Free energy landscape of A-DNA to B-DNA conversion in aqueous solution. J Am Chem Soc 2005 1.44
44 Src kinase conformational activation: thermodynamics, pathways, and mechanisms. PLoS Comput Biol 2008 1.43
45 Structural determinants of proton blockage in aquaporins. J Mol Biol 2004 1.43
46 Simulated x-ray scattering of protein solutions using explicit-solvent models. J Chem Phys 2009 1.43
47 The ionization state and the conformation of Glu-71 in the KcsA K(+) channel. Biophys J 2002 1.41
48 High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. J Phys Chem Lett 2011 1.41
49 Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field. J Phys Chem B 2005 1.39
50 Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. J Chem Theory Comput 2010 1.39
51 Atomistic view of the conformational activation of Src kinase using the string method with swarms-of-trajectories. Biophys J 2009 1.37
52 Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix. J Phys Chem B 2008 1.36
53 In search of a consensus model of the resting state of a voltage-sensing domain. Neuron 2011 1.36
54 Grand canonical Monte Carlo simulations of water in protein environments. J Chem Phys 2004 1.36
55 Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. J Chem Theory Comput 2010 1.35
56 Architecture and assembly of the Gram-positive cell wall. Mol Microbiol 2013 1.34
57 Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD). J Chem Theory Comput 2009 1.30
58 On the potential functions used in molecular dynamics simulations of ion channels. Biophys J 2002 1.29
59 On the structural basis of modal gating behavior in K(+) channels. Nat Struct Mol Biol 2010 1.29
60 Three-dimensional architecture of membrane-embedded MscS in the closed conformation. J Mol Biol 2007 1.27
61 Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations. J Am Chem Soc 2009 1.25
62 Standard binding free energies from computer simulations: What is the best strategy? J Chem Theory Comput 2013 1.24
63 Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. J Chem Theory Comput 2010 1.24
64 On the origin of the electrostatic potential difference at a liquid-vacuum interface. J Chem Phys 2008 1.23
65 On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases. Proc Natl Acad Sci U S A 2007 1.21
66 Intermediate state trapping of a voltage sensor. J Gen Physiol 2012 1.20
67 Ion selectivity of the KcsA channel: a perspective from multi-ion free energy landscapes. J Mol Biol 2010 1.19
68 The activated state of a sodium channel voltage sensor in a membrane environment. Proc Natl Acad Sci U S A 2010 1.18
69 Building Markov state models along pathways to determine free energies and rates of transitions. J Chem Phys 2008 1.18
70 Molecular dynamics simulations of the influenza hemagglutinin fusion peptide in micelles and bilayers: conformational analysis of peptide and lipids. J Mol Biol 2005 1.16
71 Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck. Proteins 2007 1.16
72 Rapid intracellular TEA block of the KcsA potassium channel. Biophys J 2004 1.15
73 Hydration number, topological control, and ion selectivity. J Phys Chem B 2009 1.15
74 Recovery from slow inactivation in K+ channels is controlled by water molecules. Nature 2013 1.15
75 Explaining why Gleevec is a specific and potent inhibitor of Abl kinase. Proc Natl Acad Sci U S A 2013 1.14
76 A theoretical study of aqueous solvation of K comparing ab initio, polarizable, and fixed-charge models. J Chem Theory Comput 2007 1.13
77 Mechanism of intracellular block of the KcsA K+ channel by tetrabutylammonium: insights from X-ray crystallography, electrophysiology and replica-exchange molecular dynamics simulations. J Mol Biol 2006 1.12
78 Long-pore electrostatics in inward-rectifier potassium channels. J Gen Physiol 2008 1.12
79 Two mechanisms of ion selectivity in protein binding sites. Proc Natl Acad Sci U S A 2010 1.12
80 Gramicidin channels. IEEE Trans Nanobioscience 2005 1.12
81 Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol. J Lipid Res 2006 1.08
82 Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases. Proteins 2009 1.08
83 Many-body polarization effects and the membrane dipole potential. J Am Chem Soc 2009 1.06
84 Simulating electron spin resonance spectra of nitroxide spin labels from molecular dynamics and stochastic trajectories. J Chem Phys 2008 1.06
85 Comment on "Probing the thermodynamics of competitive ion binding using minimum energy structures". J Phys Chem B 2012 1.05
86 A structural model for K2P potassium channels based on 23 pairs of interacting sites and continuum electrostatics. J Gen Physiol 2009 1.05
87 AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATA. J Chem Theory Comput 2013 1.05
88 A conformational intermediate in glutamate receptor activation. Neuron 2013 1.05
89 Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme. J Phys Chem B 2013 1.04
90 The binding of antibiotics in OmpF porin. Structure 2012 1.04
91 Molecular dynamics investigation of the ω-current in the Kv1.2 voltage sensor domains. Biophys J 2012 1.03
92 Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome. J Phys Chem B 2010 1.03
93 Efficient determination of protein-protein standard binding free energies from first principles. J Chem Theory Comput 2013 1.02
94 Critical assessment of a proposed model of Shaker. FEBS Lett 2004 1.02
95 Binding specificity of SH2 domains: insight from free energy simulations. Proteins 2009 1.02
96 Ion selectivity of alpha-hemolysin with beta-cyclodextrin adapter. II. Multi-ion effects studied with grand canonical Monte Carlo/Brownian dynamics simulations. J Phys Chem B 2010 1.02
97 Atomic constraints between the voltage sensor and the pore domain in a voltage-gated K+ channel of known structure. J Gen Physiol 2008 1.02
98 A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. J Phys Chem B 2013 1.01
99 Structural basis of a protein partner switch that regulates the general stress response of α-proteobacteria. Proc Natl Acad Sci U S A 2012 1.00
100 Determination of membrane-insertion free energies by molecular dynamics simulations. Biophys J 2012 0.99
101 On the utilization of energy minimization to the study of ion selectivity. Biophys J 2009 0.99
102 RNA structure determination using SAXS data. J Phys Chem B 2010 0.99
103 Free energy and kinetics of conformational transitions from Voronoi tessellated milestoning with restraining potentials. J Chem Theory Comput 2009 0.98
104 Comment on "Free energy simulations of single and double ion occupancy in gramicidin A" [J. Chem. Phys. 126, 105103 (2007)]. J Chem Phys 2008 0.98
105 Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: assessing entropic and environmental effects. J Comput Chem 2007 0.96
106 Constant electric field simulations of the membrane potential illustrated with simple systems. Biochim Biophys Acta 2011 0.96
107 Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion. J Am Chem Soc 2013 0.96
108 Structural refinement of membrane proteins by restrained molecular dynamics and solvent accessibility data. Biophys J 2008 0.95
109 Thermodynamic coupling between activation and inactivation gating in potassium channels revealed by free energy molecular dynamics simulations. J Gen Physiol 2011 0.94
110 Simulations of anionic lipid membranes: development of interaction-specific ion parameters and validation using NMR data. J Phys Chem B 2013 0.93
111 Protonation of key acidic residues is critical for the K⁺-selectivity of the Na/K pump. Nat Struct Mol Biol 2011 0.93
112 Selectivity of externally facing ion-binding sites in the Na/K pump to alkali metals and organic cations. Proc Natl Acad Sci U S A 2010 0.92
113 Ion selectivity of alpha-hemolysin with a beta-cyclodextrin adapter. I. Single ion potential of mean force and diffusion coefficient. J Phys Chem B 2010 0.92
114 Computing conformational free energy by deactivated morphing. J Chem Phys 2008 0.92
115 Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores. J Comput Chem 2011 0.92
116 Computational analysis of the binding specificity of Gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinases. J Am Chem Soc 2013 0.91
117 Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. I: molecular dynamics simulations. J Phys Chem B 2011 0.90
118 Molecular dynamics simulations of the Cx26 hemichannel: insights into voltage-dependent loop-gating. Biophys J 2012 0.90
119 Six-site polarizable model of water based on the classical Drude oscillator. J Chem Phys 2013 0.90
120 Quantitative analysis of the water occupancy around the selectivity filter of a K+ channel in different gating modes. J Am Chem Soc 2014 0.89
121 A variable residue in the pore of Kv1 channels is critical for the high affinity of blockers from sea anemones and scorpions. J Biol Chem 2005 0.86
122 Cation-selective pathway of OmpF porin revealed by anomalous X-ray diffraction. J Mol Biol 2009 0.86
123 CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application. J Chem Inf Model 2012 0.86
124 Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials. J Mol Recognit 2010 0.85
125 Accurate Molecular Polarizabilities Based on Continuum Electrostatics. J Chem Theory Comput 2008 0.85
126 Mechanism of Cd2+ coordination during slow inactivation in potassium channels. Structure 2012 0.85
127 Computational study of Gleevec and G6G reveals molecular determinants of kinase inhibitor selectivity. J Am Chem Soc 2014 0.84
128 Voltage profile along the permeation pathway of an open channel. Biophys J 2010 0.84
129 A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide. J Am Chem Soc 2010 0.83
130 Eppur si muove! The 2013 Nobel Prize in Chemistry. Structure 2013 0.82
131 A computational study of barium blockades in the KcsA potassium channel based on multi-ion potential of mean force calculations and free energy perturbation. J Gen Physiol 2013 0.81
132 Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields. J Chem Phys 2013 0.81
133 Computational study of the "DFG-flip" conformational transition in c-Abl and c-Src tyrosine kinases. J Phys Chem B 2015 0.81
134 Simulating the distance distribution between spin-labels attached to proteins. J Phys Chem B 2015 0.80
135 Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations. J Gen Physiol 2013 0.80
136 Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. II: nuclear magnetic resonance experiments. J Phys Chem B 2011 0.79
137 EROS: Better than SAXS! Structure 2011 0.78
138 Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions. J Comput Chem 2010 0.78
139 Structure and electrostatic property of cytoplasmic domain of ZntB transporter. Protein Sci 2009 0.78
140 Energetics of double-ion occupancy in the gramicidin A channel. J Phys Chem B 2010 0.78
141 Molecular dynamics study of a polymeric reverse osmosis membrane. J Phys Chem B 2009 0.78
142 One channel: open and closed. Structure 2005 0.77
143 Structural biology: One domain, multiple conformations. Nat Chem Biol 2011 0.75
144 Understanding Atomic-Scale Behavior of Liquid Crystals at Aqueous Interfaces. J Chem Theory Comput 2016 0.75
145 Machine Learning Force Field Parameters from Ab Initio Data. J Chem Theory Comput 2017 0.75
146 Markov state and diffusive stochastic models in electron spin resonance. Adv Exp Med Biol 2014 0.75
147 A proton-controlled check valve for sodium ion transport. Nat Chem Biol 2007 0.75