Benoit Roux to Models, Molecular
This is a "connection" page, showing publications Benoit Roux has written about Models, Molecular.
Connection Strength
2.706
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CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Adv Protein Chem Struct Biol. 2014; 96:235-65.
Score: 0.318
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Using Markov models to simulate electron spin resonance spectra from molecular dynamics trajectories. J Phys Chem B. 2008 Sep 04; 112(35):11014-27.
Score: 0.209
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Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels. Biophys Chem. 2006 Dec 01; 124(3):251-67.
Score: 0.179
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Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields. Biophys J. 2006 May 15; 90(10):3447-68.
Score: 0.176
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On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation. J Gen Physiol. 2004 Dec; 124(6):679-90.
Score: 0.162
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Extracellular blockade of K(+) channels by TEA: results from molecular dynamics simulations of the KcsA channel. J Gen Physiol. 2001 Aug; 118(2):207-18.
Score: 0.128
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Open and Closed Structures of a Barium-Blocked Potassium Channel. J Mol Biol. 2020 08 07; 432(17):4783-4798.
Score: 0.119
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Membrane Anchoring of Hck Kinase via the Intrinsically Disordered SH4-U and Length Scale Associated with Subcellular Localization. J Mol Biol. 2020 04 17; 432(9):2985-2997.
Score: 0.115
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Proton Countertransport and Coupled Gating in the Sarcoplasmic Reticulum Calcium Pump. J Mol Biol. 2018 12 07; 430(24):5050-5065.
Score: 0.106
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Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J Mol Biol. 1997 Sep 26; 272(3):423-42.
Score: 0.098
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Ion channels and ion selectivity. Essays Biochem. 2017 05 09; 61(2):201-209.
Score: 0.096
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Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations. J Chem Phys. 2014 May 14; 140(18):184114.
Score: 0.078
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Molecular dynamics simulations of the gramicidin channel. Annu Rev Biophys Biomol Struct. 1994; 23:731-61.
Score: 0.076
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Locking the active conformation of c-Src kinase through the phosphorylation of the activation loop. J Mol Biol. 2014 Jan 23; 426(2):423-35.
Score: 0.075
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Ion binding sites and their representations by reduced models. J Phys Chem B. 2012 Jun 14; 116(23):6966-79.
Score: 0.068
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Structural dynamics of the magnesium-bound conformation of CorA in a lipid bilayer. Structure. 2010 Jul 14; 18(7):868-78.
Score: 0.060
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Perspectives on: molecular dynamics and computational methods. J Gen Physiol. 2010 Jun; 135(6):547-8.
Score: 0.059
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CHARMM: the biomolecular simulation program. J Comput Chem. 2009 Jul 30; 30(10):1545-614.
Score: 0.056
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Structure of gramicidin a in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data. J Am Chem Soc. 2003 Aug 13; 125(32):9868-77.
Score: 0.037
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Atomic proximity between S4 segment and pore domain in Shaker potassium channels. Neuron. 2003 Jul 31; 39(3):467-81.
Score: 0.037
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What can be deduced about the structure of Shaker from available data? Novartis Found Symp. 2002; 245:84-101; discussion 101-8, 165-8.
Score: 0.033
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Energetics of ion conduction through the K+ channel. Nature. 2001 Nov 01; 414(6859):73-7.
Score: 0.033
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Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell. 2001 Apr 06; 105(1):115-26.
Score: 0.031
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Molecular dynamics of the KcsA K(+) channel in a bilayer membrane. Biophys J. 2000 Jun; 78(6):2900-17.
Score: 0.030
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The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations. Science. 1999 Jul 02; 285(5424):100-2.
Score: 0.028
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Statistical mechanical equilibrium theory of selective ion channels. Biophys J. 1999 Jul; 77(1):139-53.
Score: 0.028
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Molecular dynamics study of calbindin D9k in the apo and singly and doubly calcium-loaded states. Proteins. 1998 Nov 01; 33(2):265-84.
Score: 0.027
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Structure and dynamics of a proton wire: a theoretical study of H+ translocation along the single-file water chain in the gramicidin A channel. Biophys J. 1996 Jul; 71(1):19-39.
Score: 0.023
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Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer. Proteins. 1996 Jan; 24(1):92-114.
Score: 0.022
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Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water. Biophys J. 1995 Jan; 68(1):25-39.
Score: 0.020
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A molecular dynamics study of gating in dioxolane-linked gramicidin A channels. Biophys J. 1994 Oct; 67(4):1370-86.
Score: 0.020
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Dynamics transitions at the outer vestibule of the KcsA potassium channel during gating. Proc Natl Acad Sci U S A. 2014 Feb 04; 111(5):1831-6.
Score: 0.019
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Structure and dynamics of bacteriorhodopsin. Comparison of simulation and experiment. FEBS Lett. 1993 Aug 02; 327(3):256-60.
Score: 0.018
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Configurational distribution of denatured phosphoglycerate kinase. J Mol Biol. 1993 Jun 05; 231(3):840-8.
Score: 0.018
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Ion transport in a model gramicidin channel. Structure and thermodynamics. Biophys J. 1991 May; 59(5):961-81.
Score: 0.016
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Nanosculpting reversed wavelength sensitivity into a photoswitchable iGluR. Proc Natl Acad Sci U S A. 2009 Apr 21; 106(16):6814-9.
Score: 0.014
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The normal modes of the gramicidin-A dimer channel. Biophys J. 1988 Mar; 53(3):297-309.
Score: 0.013
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Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus. J Mol Biol. 2002 Aug 16; 321(3):459-78.
Score: 0.009
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Imaging the electrostatic potential of transmembrane channels: atomic probe microscopy of OmpF porin. Biophys J. 2002 Mar; 82(3):1667-76.
Score: 0.008
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Lipid-mediated interactions between intrinsic membrane proteins: a theoretical study based on integral equations. Biophys J. 2000 Dec; 79(6):2867-79.
Score: 0.008
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A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. Biophys J. 2000 Aug; 79(2):788-801.
Score: 0.007
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Anchoring of a monotopic membrane protein: the binding of prostaglandin H2 synthase-1 to the surface of a phospholipid bilayer. Eur Biophys J. 2000; 29(6):439-54.
Score: 0.007
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Simulation analysis of the retinal conformational equilibrium in dark-adapted bacteriorhodopsin. Biophys J. 1999 Apr; 76(4):1909-17.
Score: 0.007
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Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane. Biophys J. 1998 Oct; 75(4):1603-18.
Score: 0.007
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High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints. Structure. 1997 Dec 15; 5(12):1655-69.
Score: 0.006
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Fine mapping of neutralization epitopes on duck hepatitis B virus (DHBV) pre-S protein using monoclonal antibodies and overlapping peptides. Virology. 1993 Jan; 192(1):217-23.
Score: 0.004