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Refereed Journals
1. B. ROUX, and R. SAUVE, "A General Solution to the Time Interval Omission Applied to Single Channel Analysis", Biophys. J, 48, 149-158, 1985.
2. B. ROUX and M. KARPLUS, "The Normal Modes of the Gramicidin A Dimer", Biophys. J. 53, 297-309, (1987).
3. B. ROUX, H.A. YU and M. KARPLUS "Molecular Basis for the Born Model of Ion Solvation", J. Phys. Chem. 94, 4683-4688, 1990.
4. H.A. YU, B. ROUX and M. KARPLUS, "Solvation Thermodynamics: An approach from Analytic Temperature Derivatives", J. Chem. Phys. 92, 5020-5033 (1990).
5. B. ROUX, R. BRÜSCHWEILER and R.R. ERNST, "The structures of Gramicidin A in dimethylsulphoxyde/acetone", Eur. J. Biochem. 194, 57-60 (1990).
6. J.E. STRAUB, B.J. BERNE and ROUX B., "Spatial Dependence of Time-Dependent Friction for Pair Diffusion in a Simple Fluid", J. Chem. Phys. 93, 6804-6812 (1990).
7. B. ROUX and M. KARPLUS, "Ion Transport in a Gramicidin-like Channel: Structure and thermodynamics", Biophys. J. 59, 961-980 (1991).
8. B. ROUX and M. KARPLUS, "Ion Transport in a Gramicidin-like Channel: Dynamics and Mobility", J. Phys. Chem. 95, 4856-4868 (1991).
9. R. BRÜSCHWEILER, B. ROUX, M. BLACKLEDGE, C. GRIESINGER, M.KARPLUS, and R.R. ERNST, "Influence of Rapid Intramolecular Motions on NMR Cross-Relaxation Rates. A Molecular Dynamics Study of Antamanide in Solution"., J. Am. Chem. Soc. 114, 2289-2302, (1992).
10. P. CALMETTES, B. ROUX, D. DURAND, M. DESMADRIL and J.C. SMITH, "Configurational Distribution of Denatured Phosphoglycerate Kinase", J. Mol. Biol. 231, 840-848 (1993).
11. B. ROUX and M. KARPLUS, "Ion Transport in the Gramicidin Channel: Free Energy of the Solvated Right-Handed Dimer in a Model Membrane", J. Am. Chem. Soc. 115, 3250-3262 (1993).
12. A. THOMAS, B. ROUX, J.C. SMITH, "Computer Simulations of the Flexibility of a Series of Synthetic Peptide Analogues", Biopol. 33, 1249-1270 (1993).
13. M. FERRAND, G. ZACCAI, M. NINA, J.C. SMITH, C. ETCHEBEST and ROUX, B., "Structure and Dynamics of Bacteriorhodopsin - Comparison of Simulation and Experiment", FEBS 327, 256-260 (1993).
14. M. NINA, J.C. SMITH and B. ROUX, "Ab Initio Quantum Chemical Analysis of Water-Schiff Base Interactions in Bacteriorhodopsin", J. Mol. Struc. (Theochem.) 286, 231-245 (1993).
15. B. ROUX, "Nonadditivity in Cation-Peptide Interactions: A Molecular Dynamics and Ab Initio Study of Na+ in the Gramicidin Channel", Chem. Phys. Lett. 212, 231- 240 (1993).
16. B. ROUX and M. KARPLUS, "Molecular Dynamics Simulations of the Gramicidin Channel", Ann. Rev. Biomol. Struc. Dyn. 23, 731-761 (1994).
17. T.B. WOOLF and B. ROUX, "The Conformational Flexibility of o-Phosphorylcholine and o-Phosphorelethanolamine: A Molecular Dynamics Study of Solvation Effects", J. Am. Chem. Soc. 116, 5916-5926 (1994).
18. D. BEGLOV and B. ROUX, "Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations", J. Chem. Phys. 100, 9050-9063 (1994). [ pdf ]
19. S. CROUZY, T.B. WOOLF and B. ROUX, "Gating of an Ion Channel: A Molecular Dynamics Study of Dioxolane-linked Gramicidin A Channels", Biophys. J. 67, 1370-1386 (1994).
20. T.B. WOOLF and B. ROUX, "Molecular Dynamics Simulation of the Gramicidin A Channel in a Phospholipid Bilayer", Proc. Natl. Acad. Sci. USA 91, 11631-11635 (1994). [ pdf ]
21. M. NINA, B. ROUX and J.C. SMITH, "Functional Interactions in Bacteriorhodopsin: A theoretical analysis of retinal hydrogen bonding with water", Biophys. J. 68, 25-39 (1995).
22. D. BEGLOV and B. ROUX, "Dominant Solvation Effects from Primary Shell of Hydration: Approximation for Molecular Dynamics Simulations", Biopol. 35, 171-178 (1995).
23. B. ROUX and M. KARPLUS, "Potential Energy Function For Cations-Peptide Interactions: An Ab Initio Study"J. Comp. Chem. 16, 690-704 (1995).
24. B. ROUX, B. PROD'HOM and M. KARPLUS, "Ion Transport in the Gramidin Channel: Molecular Dynamics Study of Single and Double Occupancy", Biophys. J. 68, 876-892 (1995).
25. R. POMES and B. ROUX, "Quantum Effects on the Structure and Energy of a Protonated Linear Chain of Hydrogen-Bonded Water Molecules", Chem. Phys. Lett. 234, 416-624 (1995). [ pdf ]
26. T.B. WOOLF, V. MALKIN, O. MALKIN, D.R. SALAHUB and B. ROUX, "A Molecular Dynamics and Ab Initio Study of the Backbone 15N Chemical Schift Tensor of the Gramicidin Channel. Consequences for Structure Determination by Solid State NMR", Chem. Phys. Lett. 239, 186-194 (1995). [ pdf ]
27. B. ROUX, "The calculation of the potential of mean force using computer simulations", Comp. Phys. Comm. 91, 1-8 (1995). [ pdf ]
28. D. BEGLOV and B. ROUX, "Numerical solution of the HNC equation for solute of arbitrary geometry in three-dimensions ", J. Chem. Phys. 103, 360-364 (1995).
29. T.B. WOOLF and B. ROUX, "Molecular Dynamics Simulation of the Gramicidin A Channel in a Phospholipid Bilayer", PROT: Struc. Funct. Gen. 24, 92-114 (1996).
30. R. POMES and B. ROUX, "Theoretical Study of H+ Translocation along a Model Proton Wire", J. Phys. Chem. 100, 2519-2527 (1996).
31. R. POMES and B. ROUX, "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. 71, 19-39 (1996).
32. D. BEGLOV and B. ROUX, "Solvation of Complex Molecules in a Polar Liquid: An Integral Equation Theory", J. Chem. Phys. 104, 8678-8689 (1996). [ pdf ]
33. B. ROUX, M. NINA, R. POMES and J.C. SMITH, "Thermodynamics Stability of Water Molecules in the Bacteriorhodopsin Proton Channel: A Molecular Dynamics Free Energy Perturbation Study", Biophys. J. 72, 670-681 (1996).
34. K. HINSEN and B. ROUX, "A Potential Function for Computer Simulation Studies of Proton Transfer in Acetylacetone", J. Comp. Chem. 106, 3567-3577 (1997).
35. B. ROUX, "Comentary: Surface Tension of Biomembranes", Biophys. J. 71, 1346-1347 (1996).
36. J.-M. PETIT, B. ROUX, X.X. Zhu and P.M. Macdonald, "A New Physical Model for the Diffusion of Solvents and Solute Probes in Polymer Solutions", Macromol. 29, 6031-6036 (1996).
37. K. HINSEN and B. ROUX, "Potential of Mean Force and Reaction Rates for Proton Transfer in Acetylacetone", J. Chem. Phys. 106, 3567-3577 (1997).
38. B. ROUX, "The molecular basis of the valence selectivity of the gramicidin channel: A molecular dynamics free energy perturbation study", Biophys. J. 71, 3177-3187 (1996).
39. A.-J. PETRESCU, P. CALMETTES, D. DURAND, V. RECEVEUR, M. DESMADRIL, B. ROUX and J.C. SMITH, "Small Angle Neutron Scattering of a Strongly Denatured Protein: Analysis using Random Polymer Theory", Biophys. J. 72, 335-342 (1997).
40. T.B. WOOLF and B. ROUX, "The Binding Site of Sodium in the Gramicidin A Channel: A Comparison of Molecular Dynamics Simulations with Solid State NMR Data", Biophys. J. 72, 1930-1945 (1997).
41. O. SHARAFEDDIN, K. HINSEN, T. CARRINGTON and B. ROUX, "Mixed Quantum-Classical Simulation Methods Applied to Intramolecular Proton Transfer in Acetylacetone", J. Comp. Chem. 18, 1760-1772 (1997).
42. M. NINA, D. BEGLOV and B. ROUX, "Atomic Born radii for continuum electrostatic calculations based on molecular dynamics free energy simulations", J. Phys. Chem. B 101, 5239-5248 (1997).
43. I. GAMBU and B. ROUX, "The Interaction of K+ with a Phospholipid Bilayer: A Molecular Dynamics Study", J. Phys. Chem. B 101, 6066-6072 (1997).
44. D. BEGLOV and B. ROUX, "An Integral Equation to Describe the Solvation of Polar Molecules in Liquid Water", J. .Phys. Chem. B 101, 7821-7826 (1997). [ pdf ]
45. D. MOHANTY, R. ELBER, D. THIRUMALAI, D. BEGLOV AND B.ROUX, "Kinetic of peptide folding: Computer simulations of SYPFDV and peptide variants in water", J. Mol. Biol. 272, 423-442 (1997).
46. B. ROUX, "The influence of the membrane potential on the free energy of an intrinsic protein", Biophys. J. 73, 2980-2989 (1997). [ pdf ]
47. K. BELOHORCOVA, J.H. DAVIS, T.B. WOOLF and B. ROUX, "Structure and dynamics of an amphiphilic peptide in a phospholipid bilayer: a molecular dynamics study", Biophys. J. 73, 3039-3055 (1997).
48. J. BAUDRY, S. CROUZY, B. ROUX and J.C. SMITH, "Quantum chemical and free energy simulation analysis of reinal conformational energetics", J. Chem. Inf. Comp. Sci. 37, 1018-1024 (1997). [ pdf ]
49. R.R. KETCHEM, B. ROUX and T.A. CROSS, "High resolution refinement of a solid-state NMR-derived structure of gramicidin A in a lipid bilayer environment", Prot .Sci. 5, 1655-1669 (1997).
50. W. IM, D. BEGLOV and B. ROUX, "Continuum solvation model: Electrostatic forces from numerical solutions to the Poisson-Bolztmann equation", Comp. Phys. Comm. 111, 59-75 (1998). [ pdf ]
51. A.D MACKERELL, D. BASHFORD, M BELLOT, R.L. DUNBRACK, J.D. EVANSECK, M.J. FIELD, J. GAO, H. GUO, S. HA, D. JOSEPH-MCARTHY, L. KUCHNIR, K. KUCZERA, F.T.K. LAU, C. MATTOS, S. MICHNICK, T. NOG, D.T. NGUYEN, B. PRODHOM, W.E. REIHER, B. ROUX, M. SCHLENKRICH, J.C. SMITH, R. STOTE, J. STRAUB, M. WATANABE, J. WIORKIEWICZ-KUCZERA AND M. KARPLUS. "All-atom empirical potential for molecular modeling and dynamics studies of proteins", J. Phys. Chem. B 102, 3586-3616 (1998).
52. B. ROUX, "Molecular dynamics Simulations of Ion Channels: How far we have gone and where are we heading?", Biophys. J. 74, 2744-2745 (1998).
[ pdf ]
53. R. POMES and B. ROUX, "Free energy profiles for H+ conduction along hydrogen-bonded chains of water molecules", Biophys. J. 75, 33-40 (1998). [ pdf ]
54. S. BERNECHE, M. NINA and B. ROUX, "Molecular dynamics of melittin in a dimyristoyl phosphatidylcholine bilayer membrane", Biophys. J. 75, 1603-1618 (1998). [ pdf ]
55. S. MARCHAND and B. ROUX, "Molecular dynamics study of calbindin D9K in the apo, singly and doubly calcium-loaded states", PROT. Struc. Funct. Gen. 33, (1998). [ pdf ]
56. N. CHAKRABARTI, T. CARRINGTON and B. ROUX, "Rate constants in quantum mechanical systems: A rigorous and practical path-integral formulation for computer simulations", Chem. Phys. Lett. 293, 209-220 (1998). [ pdf ]
57. B. ROUX and T. SIMONSON, "Implicit solvent models", Biophys. Chem. 78, 1-20 (1999).
[ pdf ]
58. M. NINA, W. IM and B. ROUX, "Optimized radii for protein solvation forces based on continuum electrostatics", Biophys. Chem. 78, 89-96 (1999). [ pdf ]
59. P. LAGUE, M.J. ZUCKERMANN and B. ROUX, "Protein inclusions in lipid membranes: A theory based on the hypernetted chain integral equation", J. Chem. Soc. Farad. Trans. 111, 165-172 (1999).
60. J. BAUDRY, S. CROUZY, B. ROUX and J.C. SMITH, "Simulation analysis of the retinal conformational equilibrium in dark-adapted bacteriorhodopsin", Biophys. J. 76, 1909-2927 (1999).
61. B. ROUX, "Statistical mechanical equilibrium theory of selective ion channels", Biophys. J. 77, 139-153 (1999). [ pdf ]
62. B. ROUX and R. MacKinnon, "The cavity and pores helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations", Science 285, 100-102 (1999). [ pdf ]
63. S. CROUZY, J. BAUDRY, J.C. SMITH and B. ROUX, "Efficient calculation of 2-dimensional adiabatic and free energy maps: application to the isomerization of the C13=C14 and C15=N16 bonds in the retinal of bacteriorhodopsin", J. Comp. Chem. 20, 1644-1658 (1999).
64. R. POMES, E. EISENMESSER, C.B. POST and B. ROUX, "Calculating excess chemical potentials using dynamical simulations in the fourth dimension", J. Chem. Phys. 111, 3387-3395 (1999).
65. Q. DU, D. BEGLOV and B. ROUX, "Solvation free energy of polar and non-polar molecules in water: An extended site-reduced integral equation theory", J. Chem. B 104, 796-805 (1999). [ pdf ]
66. B. ROUX, "Theories of ion permeation: A chaser", J. Gen. Physiol. 114, 605-608 (1999). [ pdf ]
67. B. ROUX, "Proton wires are different", Biophys., J. 77, 2331-2332 (1999). [ pdf ]
68. S. BERNECHE and B. ROUX, "Molecular dynamics of the KcsA K+ channel in a bilayer membrane", Biophys. J. 78, 2900-2917 (2000). [ pdf ]
69. W. IM, S. SEEFELD and B. ROUX, "A grand canonical monte carlo-Brownian dynamics algorithm for simulating ion channels", Biophys. J. 79, 788-801 (2000). [ pdf ]
70. S.S. SHOBANA, B. ROUX and O.S. ANDERSEN, "Free energy simulations: thermodynamic reversibility and variability", J. Phys. Chem. B 104, 5179-5190 (2000). [ pdf ]
71. M. NINA, S. BERNECHE and B. ROUX, "Anchoring of a monotopic membrane protein: the binding of prostaglandin H2 synthase-1 to the surface of a phospholipid bilayer", Eur. Biophys. J. 29, 439-454 (2000). [ pdf ]
72. B. ROUX, S. BERNECHE and W. IM, "Ion channel, permeation and electrostatics: Insight into the function of KcsA", Biochem. 39, 13295-13306 (2000). [ pdf ]
73. P. LAGUE, M.J. ZUCKERMANN and B. ROUX, "Lipid-mediated interactions between membrane proteins: A theoretical study based on integral equations", Biophys. J. 79, 2867-2879 (2000). [ pdf ]
74. M.F. SCHUMAKER, R. POMES and B. ROUX, "A combined molecular dynamics diffusion model of single proton conduction through gramicidin", Biophys. J. 79, 2840-2857 (2000). [ pdf ]
75. M. SOUAILLE and B. ROUX, "Extension to the Weighted Histogram Analysis Method: Combining Umbrella Sampling with Free Energy Calculations", Comput. Phys. Comm. 135, 40-57 (2001). [ pdf ]
76. M.F. SCHUMAKER, R. POMES and B. ROUX, "Framework Model for Single Proton Conduction Through Gramicidin", Biophys. J. 80, 12-30 (2001). [ pdf ]
77. P. LAGUE, M.J. ZUCKERMAN and B. ROUX, "Lipid-Mediated Interactions Between Intrinsic Membrane Proteins: Dependence on Protein Size and Lipid Composition", Biophys. J. 81, 276-284 (2001). [ pdf ]
78. M.A. YOUNG, S. GONFLONI, G. SUPERTI-FURGA, B. ROUX and J. KURIYAN, "Dynamic Coupling Between the SH2 and SH3 Domains of c-Rc and Hck Underlies Their Inactivation by C-terminal Tyrosine Phosphorylation", Cell 105, 115-126 (2001). [ pdf ]
79. W. IM, S. BERNECHE and B. ROUX, "Generalized Solvent Boundary Potential for Computer Simulations", J. Chem. Phys. 114, 2924-2937 (2001). [ pdf ]
80. S. CROUZY, S. BERNECHE and B. ROUX, "Extracellular Blockade of K+ Channels by TEA: Results from Molecular Dynamics Simulations of the KcsA Channel", J. Gen. Physiol. 118, 207-216 (2001). [ pdf ]
81. W. IM and B. ROUX, "Brownian Dynamics Solutions of Ions Channels: A General Treatment of Electrostatic Reaction Fields for Molecular Pores of Arbitrary Geometry", J. Chem. Phys. 115, 4850-4861 (2001). [ pdf ]
82. S. BERNECHE and B. ROUX, "Energetics of Ion Conduction through the K+ Channel", Nature 414, 73-77 (2001). [ pdf ]
83. S. BERNECHE and B. ROUX, "The Ionization State and the Conformation of Glu-71 in the KcsA K(+) Channel.", Biophys. J. 82, 772-780 (2002). [ pdf ]
84. A. PHILIPPSEN, W. IM, A. ENGEL, T. SCHIRMER, B. ROUX, D.J. MULLER. "Imaging the Electrostatic Potential of Transmembrane Channels: Atomic Probe Microscopy of OmpF Porin", Biophys. J. 82, 1667-1676 (2002). [ pdf ]
85. B. ROUX and S. BERNECHE, "On the potential functions used in molecular dynamics simulations of ion channels", Biophys. J. 82, 1681-1684 (2002). [ pdf ]
86. B. ROUX "Theoretical and Computational Models of Ion Channels", Curr. Op. Struc. Biol.12, 182-189 (2002). [ pdf ]
87. R. POMES and B. ROUX, "Molecular Mechanism of H+ Conduction in the Single-File Water Chain of the Gramicidin Channel", Biophys. J. 82, 2304-2316 (2002). [ pdf ]
88. B. ROUX, "Computational Studies of the Gramicidin Channel", Acc. Chem. Res. 35, 366-375 (2002). [ pdf ]
89. W. IM and B. ROUX. "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. 319, 1177-1197 (2002). [ pdf ]
90. M. SIMOES, L. GARNEAU, H. KLEIN, U. BANDERALI, F. HOBEILA, B. ROUX, L. PARENT and R. SAUVE. "Cysteine Mutagenesis and Computer Modeling of the S6 Region of an Intermediate Conductance IKCa Channel", J. Gen. Physiol. 120, 99-116 (2002). [ pdf ]
91. W. IM and B. ROUX, "Ion Permeation and Selectivity of OmpF Porin: A Theoretical Study Based on Molecular Dynamics, Brownian Dynamics, and Continuum Electrodiffusion Theory.", J. Mol. Biol.322, 851-869 (2002). [ pdf ]
92. N. K. BANAVALI, W. IM and B. ROUX, "Electrostatic free energy calculations using the generalized boundary potential", J. Chem. Phys. 117, 7381-7388 (2002). [ pdf ]
93. L. PARENT, R. SAUVE, S. BERNECHE and B. ROUX "A bas les barrieres d'energie dans les canaux potassiques!", Med. Sci. 18, 604-609 (2002). [ pdf ]
94. N. K. BANAVALI and B. ROUX, "Atomic radii for continuum electrostatics calculations on nucleic acids", J. Phys. Chem. B 106, 11026-11035 (2002). [ pdf ]
95. M.A.L. ERIKSSON and B. ROUX, "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. 83, 2595-2609 (2002). [ pdf ]
96. L. YANG, W. BEARD, S. WILSON, B. ROUX, S. BROYDE, T. SCHLICK. "Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus", J. Mol. Biol. 321, 459-478 (2002). [ pdf ]
97. W.R. SILVERMAN, B. ROUX and D.M. PAPAZIAN, "Structural basis of two-stage voltage-dependent activation in K+ channels", Proc. Nat. Acad. Sci. 100, 2935-2940 (2003). [ pdf ]
98. S. BERNECHE and B. ROUX, "A Microscopic View of Ion Conduction Through the KcsA K+ Channel", Proc. Nat. Acad. Sci. 100 , 8644-8648 (2003). [ pdf ]
99. G. LAMOUREUX and B. ROUX, "Modeling Induced Polarization with Classical Drude Oscillators: Theory and Molecular Dynamics Simulation Algorithm", J. Chem. Phys. 119, 3025-3039 (2003). [ pdf ]
100. T.W. ALLEN, O.S. ANDERSEN and B. ROUX, "The structure of gramicidin A in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data", J. Am. Chem. Soc. 125, 9868-9877 (2003). [ pdf ]
101. M. LAINE, M.C.A. LIN, J.A. BANNISTER, W.R. SILVERMAN, B. ROUX and D.M. PAPAZIAN, "Atomic proximity between S4 segment and pore domain in Shaker potassium channels", Neuron 39, 467-481 (2003). [ pdf ]
102. G. LAMOUREUX, A.D. MACKERELL JR. and B. ROUX, "A Simple Polarizable Model of Water Based on Classical Drude Oscillators", J. Chem. Phys. 119, 5185-5197 (2003). [ pdf ]
103. T.W. ALLEN, O.S. ANDERSEN and B. ROUX, "Energetics of ion conduction through the gramicidin channel", Proc. Nat. Acad. Sci. 101, 117-122 (2004). [ pdf ]
104. N. CHAKRABARTI, E. TAJKHORSHID, B. ROUX and R. POMES. "Molecular Basis of Proton Blockage in Aquaporins",
Struct. 12, 65-74 (2004). [ pdf ]
105. M. LAINE, D.M. PAPAZIAN and B.ROUX, "Critical assessment of a proposed model of Shaker", FEBS Lett. 564, 257-63 (2004). [ pdf ]
106. B. ROUX, T.W. ALLEN. S. BERNECHE and W. IM. "Theoretical and computational models of biological ion channels", Quat. Rev. Biophys. 37, 15-103 (2004). [ pdf ]
107. J.D. FARALDO-GOMEZ and B. ROUX. "Electrostatics of ion stabilization in a ClC chloride channel homologue from Escherichia coli", J. Mol. Biol. 339, 981-1000 (2004). [ pdf ]
108. S.Y. NOSKOV, W. IM and B. ROUX. "Ion Permeation through the {alpha}-Hemolysin Channel: Theoretical Studies Based on Brownian Dynamics and Poisson-Nernst-Plank Electrodiffusion Theory", Biophys. J. 87, 2299-2309 (2004). [ pdf ]
109. N. CHAKRABARTI, B. ROUX and R. POMES. "Structural determinants of proton blockage in aquaporins", J. Mol. Biol. 343, 493-510 (2004). [ pdf ]
110. H.J. WOO, A.R. DINNER and B. ROUX, "Grand canonical Monte Carlo simulations of water in protein environments", J. Chem. Phys. 121, 6392-6400 (2004). [ pdf ]
111. B. ROUX and K. SCHULTEN, "Computational studies of membrane channels", Struct. 12, 1343-1351 (2004). [ pdf ]
112. S.Y. NOSKOV, S. BERNECHE and B. ROUX, "Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands", Nature 431, 830-834 (2004). [ pdf ] [ Supp Inf ]
113. Y. DENG and B. ROUX, "Hydration of Amino Acid Side Chains: Nonpolar and Electrostatic Contributions Calculated from Staged Molecular Dynamics Free Energy Simulations with Explicit Water Molecules", J. Phys. Chem. B 108, 16567-16576 (2004). [ pdf ]
114. T.W. ALLEN, O.S. ANDERSEN and B. Roux, "On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation", J. Gen. Physiol. 124, 679-690 (2004). [ pdf ]
115. V.M. ANISIMOV, G. LAMOUREUX, I.V. VOROBYOV, N. HUANG, B. ROUX, and A. D. MACKERELL Jr., "Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator" J. Chem. Theo. Comp. 1, 153-168 (2005). [ pdf ] [ Supp Inf ]
116. S.Y. NOSKOV, G. LAMOUREUX, and B. ROUX. "Molecular Dynamics Study of Hydration in Ethanol-Water Mixtures Using a Polarizable Force Field" J. Phys. Chem. B 109, 6705-6713 (2005). [ pdf ]
117. E. KUTLUAY, B. ROUX, L. HEGINBOTHAM, "Rapid intracellular TEA block of the KcsA potassium channel", Biophys. J. 88, 1018-1029 (2005). [ pdf ]
118. B. ROUX, "Ion conduction and selectivity in K+ channels", Ann. Rev. Biomol. Struc. Dyn. 34, 153-171 (2005). [ pdf ]
119. S. BERNECHE and B. ROUX, "A gate in the selectivity filter of potassium channels", Structure (Camb) 13, 591-600 (2005). [ pdf ]
120. O.S. ANDERSEN, R.E. KOEPPE 2nd and B. ROUX, "Gramicidin channels", IEEE Trans Nanobioscience 4, 10-20 (2005) [ pdf ]
121. H.-J. WOO and B. ROUX, "Chemical Theory and Computation Special Feature: Calculation of absolute protein-ligand binding free energy from computer simulations", Proc. Nat. Acad. Sci. USA 102, 6825-6830 (2005). [ pdf ] [ supp ]
122. N.K. BANAVALI and B. ROUX, "Free energy landscape of A-DNA to B-DNA conversion in aqueous solution", J. Am. Chem. Soc. 127, 6866-6876 (2005). [ pdf ]
123. B. GILQUIN, S. BRAUD, M.A. ERIKSSON, B. ROUX, T.D. BAILEY, B.T. PRIEST, M.L. GARCIA, A. MENEZ A, and S. GASPARINI. "A variable residue in the pore of Kv1 channels is critical for the high affinity of blockers from sea anemone and scorpions", J. Biol. Chem. 280, 27093-27102 (2005). [ pdf ]
124. B. CHANDA, O. K. ASAMOAH, R. BLUNCK, B. ROUX and F. BEZANILLA. "Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement", Nature 436, 852-856 (2005). [ pdf ]
125. B. ROUX. "The art of dissecting the function of a potassium channel", Neuron 47, 777-778 (2005). [ pdf ]
126. J.L. ROBERTSON and B. ROUX. "One channel: open and closed", Structure 10, 1398-1400 (2005). [ pdf ]
127. V. JOGINI and B. ROUX. "Electrostatics of the intracellular vestibule of K+ channels", J. Mol. Biol. 254, 272-288 (2005). [ pdf ]
128. N.K. BANAVALI and B. ROUX, "The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation", Structure 11, 1715-1723 (2005). [ pdf ]
129. P. LAGUE, B. ROUX, R.W. PASTOR, "Molecular dynamics simulations of the influenza hemagglutinin fusion peptide in micelles and bilayers: conformational analysis of peptide and lipids",
J. Mol. Biol. 354, 1129-1141 (2005). [ pdf ]
130. G. LAMOUREUX, E. HARDER, I.V. VOROBYOV, B. ROUX and A.D. MACKERELL, "A polarizable model of water for molecular dynamics simulations of biomolecules" Chem. Phys. Letters 418, 245-249 (2006). [ pdf ]
131. G. LAMOUREUX and B. ROUX, "Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field", J. Phys. Chem. B 110, 3308-3322 (2006). [ pdf ]
132. T.W. ALLEN, O.S. ANDERSEN and B. ROUX, "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). [ pdf ]
133. J.F. CORDERO-MORALES, L.G. CUELLO, Y. ZHAO, V. JOGINI, CORTES, B. ROUX and E. PEROZO, "Molecular determinants of gating at the potassium-channel selectivity filter." Nat. Struct. Mol. Biol. (2006). [ pdf ]
134. Y. DENG and B. ROUX, "Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant." J. Chem. Theor. Comput. 2 1255-1273 (2006). [ pdf ]
135. T.W. ALLEN, O.S. ANDERSEN and B. ROUX, "Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels." Biophys. Chem. 124 251-267 (2006). [ pdf ]
136. S.Y. NOSKOV and B. ROUX, "Ion selectivity in potassium channels." Biophys. Chem. 124 279-291 (2006). [ pdf ]
137. B. ROUX, "Extracellular blockade of potassium channels by TEA+: the tip of the iceberg?" J. Gen. Physiol. 128, 635-636 (2006).
138. B. ROUX, "Dissecting the coupling between the voltage sensor and pore domains." Neuron 52, 568-569 (2006).
139. M. MURCIA, J.D. FARALDO-GOMEZ, F.R. MAXFIELD and B. ROUX, "Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol." J. Lipid Res. 47, 2614-2630 (2006).
140. J. WANG, Y. DENG and B. ROUX, "Absolute Binding Free Energy Calculations using Molecular Dynamics Simulations with Restraining Potentials." Biophys. J. 91 1798-2814 (2006). [ pdf ]
141. S.Y. NOSKOV and B. ROUX, "Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels." J. Gen. Physiol. 129, 135-143 (2007).
142. J.D. FARALDO-GOMEZ, E. KUTLUAY, V. JOGINI, Y. ZHAO, L. HEGINBOTHAM and B. ROUX, "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. 365, 649-692 (2006).
143. P.E. LOPES, G. LAMOUREUX, B. ROUX and A.D. MACKERELL Jr., "Polarizable empirical force field for aromatic compounds based on the classical drude oscillator." J. Phys. Chem. B. 111, 2873-2885 (2007).
144. J.D. FARALDO-GOMEZ and B. ROUX, "Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects." J. Comput. Chem. (2007).
145. F. CAMPOS, B. CHANDA, B. ROUX and F. BEZANILLA, "Two atomic constraints unambiguously position the S4 segment relative to S1 and S2 segments in the closed state of Shaker K channel." Proc. Nat. Acad. Sci. USA (2007).
Book Chapters
B1. R. SAUVE and B. ROUX, "Comparison Between Noise and Time Interval Analysis in the Study of Single Channel Fluctuations", 9th International Conference on Noise in Physical Systems, 255-264, C.M. Van Vliet Ed., World Scientific (1987).
B2. B. ROUX and R. SAUVE, "Ionic Channels Transitions in Patch Clamp. Effects of Noise", Cahiers de l'atelier de Grenoble, 1, 170, 1984.
B3. M. NINA, B. ROUX, J.C. SMITH, "Ground State Potential Surface Calculations for Butadiene and Retinal", Structure and Function of Retinal Proteins, J.L. Rigaud Ed., Colloque INSERM, John Libbey Eurotext Ltd. 221, 17-20 (1992).
B4. J.C. SMITH, P. CALMETTES, D. DURAND, M. DESMADRIL, S. FUROIS-CORBIN, G.R. KNELLER and B. ROUX, "On the Configurations Accessible to Folded and To Denatured Proteins", NATO Advanced Research Workshop on Statistical Mechanics, Protein Structure & Substrate Interactions, S. Doniac Ed., Plenum Press, 135-145 (1994).
B5. J.C. SMITH, D. DURAND, M. FIELD, S. FUROIS-CORBIN, G.R. KNELLER, M. NINA and B. ROUX, "Supramolecular Interactions and atomic dynamics in proteins and peptide crystals. Jumps, Lattice waves and liquid-like diffusion" NATO ASI Advanced Research Workshop on Supramolecular Chemistry, G. Wippf Ed., Kluwer, 457-475 (1994).
B6. T.B. WOOLF, J. DESHARNAIS and B. ROUX, "Structure and Dynamics of the Sidechains of the Gramicidin Channel in a DMPC Bilayer" NATO ASI Advanced Research Workshop on Supramolecular Chemistry, G. Wippf Ed., Kluwer, 519-531 (1994).
B7. B. ROUX, "Theory of Transport in Ion Channels: From Molecular Dynamics Simulations to Experiments" in Computer Simulation In Molecular Biology, J. Goodefellow ed., VCH Weinheim, chap. 6, 133-169 (1995).
B8. B. ROUX and T.B. WOOLF, "Molecular Dynamics Simulation of Pf1 Coat Protein in a Phospholipid Bilayer" in Biological Membranes: A Molecular Perspective from Computation and Experiments, K. Merz and B. Roux Eds., Birkhauser Cambridge MA, 555--587 (1996).
B9. R.R. KETCHEM, B. ROUX and T.A. CROSS, "Computational Refinement through Solid State NMR and Energy Constraints of a Membrane Bound Polypeptide" in Biological Membranes: A Molecular Perspective from Computation and Experiments, K. Merz and B. Roux Eds., Birkhauser Cambridge MA, 299-322 (1996).
B10. B. ROUX and T.B. WOOLF, "Influence of Small Perturbations on the Conductance of an Ion Channel" in Progress in Cell Research, Vol. 6, M. Sokabe, A. Auerbach and F. Sigworth Eds., Elsevier Science BV, 261-268 (1997).
B11. B. ROUX and T.B. WOOLF, "Molecular dynamics simulation of gramicidin A in a phospholipid membrane: comparison with solid state NMR data" in Human to proteins, Advances in computational life Sciences vol. 2, M.T. Michalewicz ed., CSIRO publishing, 183-200 (1998).
B12. B. ROUX, "Environment of a membrane protein", in The Encyclopedia of Computational Chemistry, Schleyer, P. v. R.; Allinger, N L.; Clark,, T.; Gasteiger, J.; Kollman, P.A.; Schaefer III, H.F.; Schreiner, P. R., Eds; John Wiley & Sons, Chichester (1998). [ pdf ]
B13. A.D. MACKERELL JR., B. BROOKS, C.L. BROOKS III, L. NILSSON, Y. WON, B. ROUX AND M. KARPLUS, "CHARMM: The energy function and the program", in The Encyclopedia of Computational Chemistry, Schleter, P. v. R.; Allinger, N.L.; Clark, T.; Gasteiger, J.; Kollman, P.A.; Schaefer III, H.F.; Schreiner, P.R., Eds. ; John Wiley & Sons, Chichester (1998).
B14. B. ROUX AND S. CROUZY, "Theoretical studies of activated processes in biological ion channels, in Classical and quantum dynamics in condensed phase simulations, B.J. Berne, G. Ciccotti and D.F. Coker Eds, World Scientific Ltd., 445-462 (1998).
B15. R. ELBER, B. ROUX AND R. OLENDER. "Applications of a stochastic path integral approach to the computations of an optimal path and ensembles of trajectories", in Lecture notes in computational science and engineering, vol 4, "Computational molecular dynamics: challenges, methods, ideas". P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, and R.D. Skeel Eds., pp. 263-280, Springer-Verlag, Berlin Heidelberg (1999).
B16. J. BAUDRY, S. CROUZY, B. ROUX and J.C. SMITH, "Modelling and simulation of light-activated membrane proteins" Genomics and proteomics: proceedings, S. Suhai Ed., Plenum, New York (1999).
B17. B. ROUX, D. BEGLOV AND W. IM. "Generalized boundary potentials for computer simulations", in Simulation and theory of electrostatic interactions in solutions, L.R. Pratt and G. Hummer Eds., American Institute of Physics Conference Proceedings 492, New York (1999).
B18. B. ROUX and T.A. WOOLF, "The binding site of sodium in the gramicidin A channel", in "Gramicidin and related ion channel-forming peptides", Novartis Foundation Symposium 225, D. J. Chadwick and G. Cardew Eds., John Wiley & Sons Ltd., 113-127 (1999).
B19. B. ROUX. "Implicit solvent models", in Computational Biophysics, O. Becker, A.D. MacKerrel, B. Roux and M. Watanabe, Eds., Marcel Dekker Inc, New York, (2001). [ pdf ]
B20. B ROUX. "What can be deduced about the structure of Shaker from available data?" in "Ion channels: From atomic resolution physiology to functional genomics", Novartis Foundation Symposium 245, pp. 84-101, G. Bock Editor, John Wiley & Sons Ltd., Chichester (2002). [ pdf ]
Books Edited
Biological Membranes: A Molecular Perspective from Computation and Experiments, K. Merz and B. Roux Eds., Birkhauser Cambridge MA, (1996).
Computational Biochemistry and Biophysics , Oren M. Becker, Alexander D. MacKerell, Benoit Roux, and Masakatsu Watanabe Eds., Marcel Dekker, (2001).
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