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Benoit Roux, Ph.D. - Publications

Affiliations: 
Biochemistry and Molecular Biology University of Chicago, Chicago, IL 
Area:
computational chemistry and biophysics
Website:
http://bmb.uchospitals.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=220

485 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Fu H, Chen H, Blazhynska M, Goulard Coderc de Lacam E, Szczepaniak F, Pavlova A, Shao X, Gumbart JC, Dehez F, Roux B, Cai W, Chipot C. Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations. Nature Protocols. PMID 35277695 DOI: 10.1038/s41596-021-00676-1  0.566
2022 Faruk NF, Peng X, Freed KF, Roux B, Sosnick TR. Challenges and Advantages of Accounting for Backbone Flexibility in Prediction of Protein-Protein Complexes. Journal of Chemical Theory and Computation. 18: 2016-2032. PMID 35213808 DOI: 10.1021/acs.jctc.1c01255  0.545
2021 Song KC, Molina AV, Chen R, Gagnon IA, Koh YH, Roux B, Sosnick TR. Folding and misfolding of potassium channel monomers during assembly and tetramerization. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34413192 DOI: 10.1073/pnas.2103674118  0.759
2021 Li J, Shen R, Rohaim A, Mendoza Uriarte R, Fajer M, Perozo E, Roux B. Computational study of non-conductive selectivity filter conformations and C-type inactivation in a voltage-dependent potassium channel. The Journal of General Physiology. 153. PMID 34357375 DOI: 10.1085/jgp.202112875  0.597
2021 Brooks CL, Case DA, Plimpton S, Roux B, van der Spoel D, Tajkhorshid E. Classical molecular dynamics. The Journal of Chemical Physics. 154: 100401. PMID 33722022 DOI: 10.1063/5.0045455  0.434
2021 Thirman J, Rui H, Roux B. Elusive Intermediate State Key in the Conversion of ATP Hydrolysis into Useful Work Driving the Ca Pump SERCA. The Journal of Physical Chemistry. B. PMID 33720716 DOI: 10.1021/acs.jpcb.1c00558  0.527
2021 Baudry J, Bondar AN, Cournia Z, Parks JM, Petridis L, Roux B. Editorial: Advances in computational molecular biophysics. Biochimica Et Biophysica Acta. General Subjects. 129888. PMID 33662454 DOI: 10.1016/j.bbagen.2021.129888  0.575
2021 Ngo V, Li H, MacKerell AD, Allen TW, Roux B, Noskov S. Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel. Journal of Chemical Theory and Computation. PMID 33539082 DOI: 10.1021/acs.jctc.0c00968  0.707
2021 Li J, Shen R, Reddy B, Perozo E, Roux B. Mechanism of C-type inactivation in the hERG potassium channel. Science Advances. 7. PMID 33514547 DOI: 10.1126/sciadv.abd6203  0.576
2021 Chen P, Vorobyov I, Roux B, Allen TW. 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. PMID 33493394 DOI: 10.1021/acs.jpcb.0c08613  0.551
2020 Kim S, Oshima H, Zhang H, Kern NR, Re S, Lee J, Roux B, Sugita Y, Jiang W, Im W. CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations. Journal of Chemical Theory and Computation. PMID 33112150 DOI: 10.1021/acs.jctc.0c00884  0.487
2020 Rupakheti C, Lamoureux G, MacKerell AD, Roux B. 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. 153: 114108. PMID 32962358 DOI: 10.1063/5.0019987  0.587
2020 Rohaim A, Gong L, Li J, Rui H, Blachowicz L, Roux B. Barium blockade of the KcsA channel in open and closed conformation datasets. Data in Brief. 32: 106135. PMID 32904340 DOI: 10.1016/J.Dib.2020.106135  0.622
2020 Phillips JC, Hardy DJ, Maia JDC, Stone JE, Ribeiro JV, Bernardi RC, Buch R, Fiorin G, Hénin J, Jiang W, McGreevy R, Melo MCR, Radak BK, Skeel RD, Singharoy A, ... ... Roux B, et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of Chemical Physics. 153: 044130. PMID 32752662 DOI: 10.1063/5.0014475  0.52
2020 Rohaim A, Gong L, Li J, Rui H, Blachowicz L, Roux B. Open and closed structures of a barium-blocked potassium channel. Journal of Molecular Biology. PMID 32615129 DOI: 10.1016/J.Jmb.2020.06.012  0.592
2020 Aleksandrov AV, Roux B, MacKerell AD. p Calculations with the Polarizable Drude Force Field and Poisson-Boltzmann Solvation Model. Journal of Chemical Theory and Computation. PMID 32464053 DOI: 10.1021/Acs.Jctc.0C00111  0.346
2020 Huang L, Wright M, Yang S, Blachowicz L, Makowski L, Roux B. Glycine substitution in SH3-SH2 connector of Hck tyrosine kinase causes population shift from assembled to disassembled state. Biochimica Et Biophysica Acta. General Subjects. 1864: 129604. PMID 32224253 DOI: 10.1016/J.Bbagen.2020.129604  0.676
2020 Paul F, Meng Y, Roux B. Identification of druggable kinase target conformations using Markov model metastable states analysis of apo Abl. Journal of Chemical Theory and Computation. PMID 31999924 DOI: 10.1021/Acs.Jctc.9B01158  0.32
2020 Li J, Shen R, Hoon Koh Y, Perozo E, Roux B. Molecular Determinants of C-type Inactivation for the hERG Channel and Its Disease-associated Mutants Biophysical Journal. 118: 111a. DOI: 10.1016/J.Bpj.2019.11.755  0.572
2020 Rohaim A, Gong L, Li J, Blachowicz L, Roux B. The Open and Closed Structure of a Barium-Blocked Potassium Channel Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.2879  0.348
2020 He P, Zuchniarz J, Zhou S, Modica J, Dhindwal S, Li Y, Voth GA, Mrksich M, Dravid VP, Roux B. Modeling Synthesized Protein Megamolecules: Structure, Dynamics, and Functions Biophysical Journal. 118: 517a. DOI: 10.1016/J.Bpj.2019.11.2848  0.314
2020 Shen R, Roux B, Perozo E. The Energy Landscape of Voltage Sensing in Ci-VSP Biophysical Journal. 118: 269a. DOI: 10.1016/J.Bpj.2019.11.1550  0.54
2019 Pond MP, Eells R, Treece BW, Heinrich F, Lösche M, Roux B. Membrane anchoring of Hck kinase via the intrinsically disordered SH4-U and lengthscale associated with subcellular localization. Journal of Molecular Biology. PMID 31877324 DOI: 10.1016/J.Jmb.2019.11.024  0.332
2019 Roux B. Calculating the Effect of Membrane Thickness on the Lifetime of the Gramicidin A Channel: A Landmark. Biophysical Journal. PMID 31668331 DOI: 10.1016/J.Bpj.2019.10.005  0.345
2019 Suh D, Jo S, Jiang W, Chipot C, Roux B. String method for Protein-Protein Binding Free Energy Calculations. Journal of Chemical Theory and Computation. PMID 31593627 DOI: 10.1021/Acs.Jctc.9B00499  0.61
2019 Awoonor-Williams E, Isley WC, Dale SG, Johnson ER, Yu H, Becke AD, Roux B, Rowley CN. Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols. Journal of Computational Chemistry. PMID 31512279 DOI: 10.1002/Jcc.26064  0.725
2019 Jiang W, Chipot C, Roux B. Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual Topology Free Energy Perturbation Approach in NAMD. Journal of Chemical Information and Modeling. PMID 31411473 DOI: 10.1021/Acs.Jcim.9B00362  0.387
2019 Qi Y, Lee J, Cheng X, Shen R, Islam SM, Roux B, Im W. CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations. Journal of Computational Chemistry. PMID 31329318 DOI: 10.1002/Jcc.26032  0.517
2019 Bedrov D, Piquemal JP, Borodin O, MacKerell AD, Roux B, Schröder C. Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields. Chemical Reviews. PMID 31141351 DOI: 10.1021/Acs.Chemrev.8B00763  0.401
2019 Ellis-Guardiola K, Rui H, Beckner RL, Srivastava P, Sukumar N, Roux B, Lewis JC. Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase. Biochemistry. PMID 30786206 DOI: 10.1021/Acs.Biochem.9B00031  0.593
2019 Jekhmane S, Medeiros-Silva J, Li J, Kümmerer F, Müller-Hermes C, Baldus M, Roux B, Weingarth M. Shifts in the selectivity filter dynamics cause modal gating in K channels. Nature Communications. 10: 123. PMID 30631074 DOI: 10.1038/S41467-018-07973-6  0.407
2019 Roux B, Song K, Hoon Koh Y, Perozo E, Sosnick TR. Structural Dynamics of Potassium Channel Monomer in a Membrane Environment and Tetrameric Assembly Biophysical Journal. 116: 461a. DOI: 10.1016/J.Bpj.2018.11.2490  0.801
2019 Song KC, Koh Y, Perozo E, Roux B, Sosnick TR. Controlling the Folding and Misfolding of Potassium Channels Biophysical Journal. 116: 301a. DOI: 10.1016/J.Bpj.2018.11.1630  0.784
2019 Li J, Hoon Koh Y, Rohaim A, Perozo E, Roux B. Atomic-Level Characterization of C-Type Inactivation for Voltage-Gated Potassium Channels Shaker and hERG Biophysical Journal. 116: 14a-15a. DOI: 10.1016/J.Bpj.2018.11.121  0.58
2018 Rui H, Das A, Nakamoto R, Roux B. Proton Countertransport and Coupled Gating in the Sarcoplasmic Reticulum Calcium Pump. Journal of Molecular Biology. 430: 5050-5065. PMID 30539761 DOI: 10.1016/J.Jmb.2018.10.014  0.578
2018 Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B. Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. Journal of Chemical Theory and Computation. PMID 30480445 DOI: 10.1021/Acs.Jctc.8B01075  0.647
2018 Callahan KM, Roux B. Molecular Dynamics of Ion Conduction through the Selectivity Filter of the NaAb Sodium Channel. The Journal of Physical Chemistry. B. PMID 30351118 DOI: 10.1021/Acs.Jpcb.8B09678  0.768
2018 Loeffler HH, Bosisio S, Duarte Ramos Matos G, Suh D, Roux B, Mobley DL, Michel J. Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software. Journal of Chemical Theory and Computation. PMID 30289712 DOI: 10.1021/Acs.Jctc.8B00544  0.366
2018 Jiang W, Thirman J, Jo S, Roux B. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis. The Journal of Physical Chemistry. B. PMID 30253098 DOI: 10.1021/Acs.Jpcb.8B03277  0.61
2018 Radak BK, Suh D, Roux B. A generalized linear response framework for expanded ensemble and replica exchange simulations. The Journal of Chemical Physics. 149: 072315. PMID 30134700 DOI: 10.1063/1.5027494  0.321
2018 Li J, Ostmeyer J, Cuello LG, Perozo E, Roux B. Rapid constriction of the selectivity filter underlies C-type inactivation in the KcsA potassium channel. The Journal of General Physiology. PMID 30072373 DOI: 10.1085/Jgp.201812082  0.631
2018 Villa F, MacKerell AD, Roux B, Simonson T. Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg. The Journal of Physical Chemistry. A. PMID 29966419 DOI: 10.1021/Acs.Jpca.8B04418  0.418
2018 Aleksandrov A, Lin FY, Roux B, MacKerell AD. Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model. Journal of Computational Chemistry. PMID 29737546 DOI: 10.1002/Jcc.25345  0.37
2018 Boulanger E, Huang L, Rupakheti C, MacKerell AD, Roux B. Optimized Lennard-Jones Parameters for Drug-Like Small Molecules. Journal of Chemical Theory and Computation. PMID 29694035 DOI: 10.1021/Acs.Jctc.8B00172  0.64
2018 Lin FY, Lopes PE, Harder ED, Roux B, MacKerell AD. Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. Journal of Chemical Information and Modeling. PMID 29624370 DOI: 10.1021/Acs.Jcim.8B00132  0.394
2018 Meng Y, Gao C, Clawson DK, Atwell S, Russell M, Vieth M, Roux B. Predicting the Conformational Variability of Abl tyrosine kinase using Molecular Dynamics Simulations and Markov State Models. Journal of Chemical Theory and Computation. PMID 29474075 DOI: 10.1021/Acs.Jctc.7B01170  0.384
2018 Meng Y, Ahuja LG, Kornev AP, Taylor SS, Roux B. A Catalytically-Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation. Journal of Molecular Biology. PMID 29410316 DOI: 10.1016/J.Jmb.2018.01.019  0.309
2018 Suh D, Radak BK, Chipot C, Roux B. Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator. The Journal of Chemical Physics. 148: 014101. PMID 29306299 DOI: 10.1063/1.5004154  0.351
2018 Rui H, Das A, Roux B. The Allosteric Coupling of the Cytoplasmic Phosphorylation and Transmembrane Domain Deocclusion in the Ca2+ SERCA Pump Elucidated by Free Energy Simulations Biophysical Journal. 114: 148a. DOI: 10.1016/J.Bpj.2017.11.829  0.53
2018 Li J, Jostmey J, Perozo E, Roux B. A Universal Molecular Mechanism for C-type Inactivation in Potassium Channels Biophysical Journal. 114: 474a-475a. DOI: 10.1016/J.Bpj.2017.11.2611  0.589
2018 Rohaim A, Gong L, Li J, Rui H, Roux B. A Structural and Computational Study of Barium Blockade in the KcsA Channel Biophysical Journal. 114: 237a. DOI: 10.1016/J.Bpj.2017.11.1321  0.561
2018 Boughter CT, Roux B, Adams EJ. Investigating Phosphoantigen-Induced Conformational Change of Butyrophilin 3A1 using All-Atom Molecular Dynamics Simulations Biophysical Journal. 114: 233a. DOI: 10.1016/J.Bpj.2017.11.1295  0.335
2018 Rupakheti CR, Roux B, Dehez F, Chipot C. Modeling induction phenomena in amino acid cation– $$\pi $$ π interactions Theoretical Chemistry Accounts. 137. DOI: 10.1007/S00214-018-2376-Z  0.349
2017 Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B. Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. Journal of Chemical Theory and Computation. PMID 29111720 DOI: 10.1021/Acs.Jctc.7B00875  0.658
2017 Li J, Ostmeyer J, Boulanger E, Rui H, Perozo E, Roux B. Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for C-type inactivation. Proceedings of the National Academy of Sciences of the United States of America. PMID 28973956 DOI: 10.1073/Pnas.1706983114  0.791
2017 Fu H, Cai W, Hénin J, Roux B, Chipot C. New Coarse Variables for the Accurate Determination of Standard Binding Free Energies. Journal of Chemical Theory and Computation. PMID 28965398 DOI: 10.1021/Acs.Jctc.7B00791  0.325
2017 Gu S, Sachleben JR, Boughter CT, Nawrocka WI, Borowska MT, Tarrasch JT, Skiniotis G, Roux B, Adams EJ. Phosphoantigen-induced conformational change of butyrophilin 3A1 (BTN3A1) and its implication on Vγ9Vδ2 T cell activation. Proceedings of the National Academy of Sciences of the United States of America. PMID 28807997 DOI: 10.1073/Pnas.1707547114  0.326
2017 Li Y, Li H, Pickard FC, Narayanan B, Sen F, Chan MKY, Sankaranarayanan S, Brooks BR, Roux B. Machine Learning Force Field Parameters from Ab Initio Data. Journal of Chemical Theory and Computation. PMID 28800233 DOI: 10.1021/Acs.Jctc.7B00521  0.515
2017 Li H, Chowdhary J, Huang L, He X, MacKerell AD, Roux B. Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids. Journal of Chemical Theory and Computation. PMID 28731702 DOI: 10.1021/Acs.Jctc.7B00262  0.383
2017 Roux B. Ion channels and ion selectivity. Essays in Biochemistry. 61: 201-209. PMID 28487397 DOI: 10.1042/Ebc20160074  0.415
2017 Kratochvil HT, Maj M, Matulef K, Annen AW, Ostmeyer J, Perozo E, Roux B, Valiyaveetil FI, Zanni MT. Probing the effects of gating on the ion occupancy of the K(+) channel selectivity filter using 2D IR spectroscopy. Journal of the American Chemical Society. PMID 28472884 DOI: 10.1021/Jacs.7B01594  0.638
2017 Meng Y, Pond MP, Roux B. Tyrosine Kinase Activation and Conformational Flexibility: Lessons from Src-Family Tyrosine Kinases. Accounts of Chemical Research. PMID 28426203 DOI: 10.1021/Acs.Accounts.7B00012  0.304
2017 Dang B, Shen R, Kubota T, Mandal K, Bezanilla F, Roux B, Kent SB. Inversion of the Side-Chain Stereochemistry of Indvidual Thr or Ile Residues in a Protein Molecule: Impact on the Folding, Stability, and Structure of the ShK Toxin. Angewandte Chemie (International Ed. in English). PMID 28194851 DOI: 10.1002/Anie.201612398  0.365
2017 Gates ZP, Baxa MC, Yu W, Riback JA, Li H, Roux B, Kent SB, Sosnick TR. Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core. Proceedings of the National Academy of Sciences of the United States of America. PMID 28193869 DOI: 10.1073/Pnas.1609579114  0.561
2017 Simonson T, Hummer G, Roux B. On the Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies. The Journal of Physical Chemistry. A. PMID 28152306 DOI: 10.1021/Acs.Jpca.6B12691  0.352
2017 Das A, Rui H, Nakamoto R, Roux B. Conformational transitions and alternating-access mechanism in the sarcoplasmic reticulum calcium pump. Journal of Molecular Biology. PMID 28093226 DOI: 10.1016/J.Jmb.2017.01.007  0.593
2017 Sherani A, Jumper JM, Ozkan E, Sosnick TR, Roux B. Molecular Determinants of Specificity in the Dpr-DIP Interaction Network Biophysical Journal. 112: 53a. DOI: 10.1016/J.Bpj.2016.11.325  0.607
2017 Sánchez-Rodríguez JE, Rui H, Roux B, Holmgren M, Bezanilla F. Tuning Voltage Dependent Transitions during the Extracellular Na + Binding/Release of the Na + /K + -ATPase by External Protons Biophysical Journal. 112: 569a-570a. DOI: 10.1016/J.Bpj.2016.11.3068  0.528
2017 Rui H, Sanchez-Rodriguez J, Holmgren M, Bezanilla F, Roux B. Ion Binding and Charge Movements in the Function of the Na/K-Pump Biophysical Journal. 112: 569a. DOI: 10.1016/J.Bpj.2016.11.3067  0.539
2017 Meyer DJ, Eastman J, Rui H, Stanley K, Roux B, Gatto C, Artigas P. A Na/K Pump with Altered Stoichiometry Contributes to Brine Shrimp Adaptation to High Salinity Biophysical Journal. 112: 569a. DOI: 10.1016/J.Bpj.2016.11.3065  0.5
2017 Li J, Ostmeyer J, Perozo E, Roux B. Molecular Determinants of Structural Coupling between C-Type Inactivation and Inner Gate Opening in K + Channels Biophysical Journal. 112: 544a. DOI: 10.1016/J.Bpj.2016.11.2941  0.602
2017 Pond MP, Eells R, Blachowicz L, Heinrich F, Bezanilla F, Veglia G, Lösche M, Roux B. Structure, Dynamics, and Function of the Membrane Associated SRC Family Kinase HCK Biophysical Journal. 112: 388a-389a. DOI: 10.1016/J.Bpj.2016.11.2111  0.33
2017 Faruk NF, Jumper J, Roux B, Sosnick TR. Extending Upside , a Near-Atomic Level Model for Fast Protein Folding, for Predicting Protein-Protein Interactions Biophysical Journal. 112: 359a. DOI: 10.1016/J.Bpj.2016.11.1946  0.547
2017 Boughter CT, Roux B, Adams EJ. Probing the Conformational Dynamics of Butyrophilin 3A1 using Atomic Force Microscopy and Molecular Dynamics Simulations Biophysical Journal. 112: 203a. DOI: 10.1016/J.Bpj.2016.11.1121  0.383
2016 Ramezani-Dakhel H, Sadati M, Rahimi M, Ramirez-Hernandez A, Roux B, de Pablo JJ. Understanding Atomic-Scale Behavior of Liquid Crystals at Aqueous Interfaces. Journal of Chemical Theory and Computation. PMID 27936703 DOI: 10.1021/Acs.Jctc.6B00844  0.32
2016 Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD, Klauda JB, Qi Y, et al. CHARMM-GUI 10 years for biomolecular modeling and simulation. Journal of Computational Chemistry. PMID 27862047 DOI: 10.1002/Jcc.24660  0.758
2016 Radak BK, Roux B. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations. The Journal of Chemical Physics. 145: 134109. PMID 27782441 DOI: 10.1063/1.4964288  0.326
2016 Fajer M, Meng Y, Roux B. The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape. The Journal of Physical Chemistry. B. PMID 27715044 DOI: 10.1021/Acs.Jpcb.6B08409  0.317
2016 Lueck JD, Mackey AL, Infield DT, Galpin JD, Li J, Roux B, Ahern CA. Atomic mutagenesis in ion channels with engineered stoichiometry. Elife. 5. PMID 27710770 DOI: 10.7554/Elife.18976  0.38
2016 Kratochvil HT, Carr JK, Matulef K, Annen AW, Li H, Maj M, Ostmeyer J, Serrano AL, Raghuraman H, Moran SD, Skinner JL, Perozo E, Roux B, Valiyaveetil FI, Zanni MT. Instantaneous ion configurations in the K+ ion channel selectivity filter revealed by 2D IR spectroscopy. Science (New York, N.Y.). 353: 1040-1044. PMID 27701114 DOI: 10.1126/Science.Aag1447  0.626
2016 Dhakshnamoorthy B, Rohaim A, Rui H, Blachowicz L, Roux B. Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola. Nature Communications. 7: 12753. PMID 27678077 DOI: 10.1038/Ncomms12753  0.6
2016 Rui H, Artigas P, Roux B. The selectivity of the Na(+)/K(+)-pump is controlled by binding site protonation and self-correcting occlusion. Elife. 5. PMID 27490484 DOI: 10.7554/Elife.16616  0.595
2016 Meng Y, Shukla D, Pande VS, Roux B. Transition path theory analysis of c-Src kinase activation. Proceedings of the National Academy of Sciences of the United States of America. PMID 27482115 DOI: 10.1073/Pnas.1602790113  0.315
2016 Jo S, Suh D, He Z, Chipot C, Roux B. Leveraging the Information from Markov State Models to Improve the Convergence of Umbrella Sampling Simulations. The Journal of Physical Chemistry. B. PMID 27409349 DOI: 10.1021/Acs.Jpcb.6B05125  0.6
2016 Chen Y, Kale S, Weare J, Dinner AR, Roux B. A Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm. Journal of Chemical Theory and Computation. PMID 26918826 DOI: 10.1021/Acs.Jctc.5B00706  0.569
2016 Medovoy D, Perozo E, Roux B. Multi-ion free energy landscapes underscore the microscopic mechanism of ion selectivity in the KcsA channel. Biochimica Et Biophysica Acta. PMID 26896693 DOI: 10.1016/J.Bbamem.2016.02.019  0.81
2016 Lemkul JA, Huang J, Roux B, MacKerell AD. An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications. Chemical Reviews. PMID 26815602 DOI: 10.1021/Acs.Chemrev.5B00505  0.348
2016 Lueck JD, Mackey AL, Infield DT, Galpin JD, Li J, Roux B, Ahern CA. Author response: Atomic mutagenesis in ion channels with engineered stoichiometry Elife. DOI: 10.7554/Elife.18976.014  0.337
2016 Rui H, Artigas P, Roux B. Author response: The selectivity of the Na+/K+-pump is controlled by binding site protonation and self-correcting occlusion Elife. DOI: 10.7554/Elife.16616.017  0.516
2016 Simonson T, Roux B. Concepts and protocols for electrostatic free energies Molecular Simulation. 42: 1090-1101. DOI: 10.1080/08927022.2015.1121544  0.397
2016 Abraham SJ, Chavan T, Cheng RC, Fenollar-Ferrer C, Han W, Islam SM, Jiang T, Khantwal CM, Mathews II, Stein RA, Roux B, Forrest LR, Mchaourab HS, Tajkhorshid E, Maduke M. An Outward-Facing Open Conformational State in a CLC Transporter Biophysical Journal. 110: 178a. DOI: 10.1016/J.Bpj.2015.11.994  0.647
2016 Shen R, Li Q, Medovoy D, Meng Y, Roux B, Perozo E. Computational Characterization of Conformational Transitions in the Voltage-Sensing Domain of Ci-VSP Biophysical Journal. 110: 106a. DOI: 10.1016/J.Bpj.2015.11.629  0.816
2016 Li J, Ostmeyer J, Fajer M, Roux B. The Constricted Filter Conformation: A General Property for C-Type Inactivation of Different Potassium Channels? Biophysical Journal. 110: 104a. DOI: 10.1016/J.Bpj.2015.11.619  0.399
2016 Boulanger E, Huang L, MacKerell AD, Roux B. Improved Lennard-Jones Parameters for Accurate Molecular Dynamics Simulations Biophysical Journal. 110: 646a. DOI: 10.1016/J.Bpj.2015.11.3458  0.639
2016 Radak BK, Singharoy A, Schulten K, Roux B. Inclusion of ph Effects in Molecular Dynamics Simulations of Membranes and Membrane Proteins Biophysical Journal. 110: 646a. DOI: 10.1016/J.Bpj.2015.11.3456  0.524
2016 Islam SM, Florin G, Qi Y, Shen R, Han W, Stein RA, Schulten K, Mchaourab HS, Im W, Roux B. Structural-Function Study of Membrane Proteins with Restrained-Ensemble and Dummy Spin-Label Molecular Dynamics Simulations Biophysical Journal. 110: 644a. DOI: 10.1016/J.Bpj.2015.11.3446  0.613
2016 Meyer DJ, Eastman J, Rui H, Stanley K, Gatto C, Roux B, Artigas P. Molecular Mechanism by which Two Lysine Substitutions Alter Na/K-Pump Stoichiometry to Confer High-Salinity Adaptation in Brine Shrimp Biophysical Journal. 110: 629a. DOI: 10.1016/J.Bpj.2015.11.3371  0.557
2016 Das A, Roux B. Conformational Transitions and Alternative Access Mechanism in ATP-Driven Calcium Pump SERCA Biophysical Journal. 110: 629a. DOI: 10.1016/J.Bpj.2015.11.3369  0.406
2016 Rui H, Roux B. Binding Site Protonation and Uphill Occlusion Control the Na+/K+-Pump Selectivity Biophysical Journal. 110: 629a. DOI: 10.1016/J.Bpj.2015.11.3368  0.579
2016 Song K, Roux B, Sosnick T. Dissecting the Folding Pathway of Potassium Channel Pore Domains Biophysical Journal. 110: 394a. DOI: 10.1016/J.Bpj.2015.11.2128  0.772
2016 Li H, Singharoy A, Roux B, MacKerell A. Drude Polarizable Force Field for Modeling Divalent Cations in Biological Systems Biophysical Journal. 110: 327a. DOI: 10.1016/J.Bpj.2015.11.1760  0.405
2015 Chen Y, Roux B. Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model. Journal of Chemical Theory and Computation. 11: 3572-83. PMID 26574442 DOI: 10.1021/Acs.Jctc.5B00372  0.368
2015 Meng Y, Roux B. Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression. Journal of Chemical Theory and Computation. 11: 3523-9. PMID 26574437 DOI: 10.1021/Ct501130R  0.311
2015 Jo S, Chipot C, Roux B. Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics. Journal of Chemical Theory and Computation. 11: 2234-44. PMID 26574422 DOI: 10.1021/Ct501034W  0.611
2015 Ngo V, da Silva MC, Kubillus M, Li H, Roux B, Elstner M, Cui Q, Salahub DR, Noskov SY. Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins. Journal of Chemical Theory and Computation. 11: 4992-5001. PMID 26574284 DOI: 10.1021/Acs.Jctc.5B00524  0.693
2015 Shen R, Han W, Fiorin G, Islam SM, Schulten K, Roux B. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments. Plos Computational Biology. 11: e1004368. PMID 26505197 DOI: 10.1371/Journal.Pcbi.1004368  0.544
2015 Chen Y, Roux B. Constant-pH Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulation Method. Journal of Chemical Theory and Computation. 11: 3919-3931. PMID 26300709 DOI: 10.1021/Acs.Jctc.5B00261  0.371
2015 Castillo JP, Rui H, Basilio D, Das A, Roux B, Latorre R, Bezanilla F, Holmgren M. Mechanism of potassium ion uptake by the Na(+)/K(+)-ATPase. Nature Communications. 6: 7622. PMID 26205423 DOI: 10.1038/Ncomms8622  0.58
2015 Meng Y, Roux B. Computational study of the W260A activating mutant of Src tyrosine kinase. Protein Science : a Publication of the Protein Society. PMID 26106037 DOI: 10.1002/Pro.2731  0.31
2015 Roux B, Rui H, Das A. 49 Structure and energetics of the pumping mechanism of membrane ATPase. Journal of Biomolecular Structure & Dynamics. 33: 33-4. PMID 26103258 DOI: 10.1080/07391102.2015.1032598  0.525
2015 Lemkul JA, Roux B, van der Spoel D, MacKerell AD. Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. Journal of Computational Chemistry. 36: 1473-9. PMID 25962472 DOI: 10.1002/Jcc.23937  0.367
2015 Islam SM, Roux B. Simulating the distance distribution between spin-labels attached to proteins. The Journal of Physical Chemistry. B. 119: 3901-11. PMID 25645890 DOI: 10.1021/Jp510745D  0.319
2015 Sánchez-Rodríguez JE, Khalili-Araghi F, Miranda P, Roux B, Holmgren M, Bezanilla F. A structural rearrangement of the Na+/K+-ATPase traps ouabain within the external ion permeation pathway. Journal of Molecular Biology. 427: 1335-44. PMID 25637661 DOI: 10.1016/J.Jmb.2015.01.011  0.39
2015 Chen Y, Roux B. Generalized Metropolis acceptance criterion for hybrid non-equilibrium molecular dynamics-Monte Carlo simulations. The Journal of Chemical Physics. 142: 024101. PMID 25591332 DOI: 10.1063/1.4904889  0.352
2015 Li H, Ngo V, Da Silva MC, Salahub DR, Callahan K, Roux B, Noskov SY. Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field. The Journal of Physical Chemistry. B. 119: 9401-16. PMID 25578354 DOI: 10.1021/Jp510560K  0.801
2015 Meng Y, Lin YL, Roux B. Computational study of the "DFG-flip" conformational transition in c-Abl and c-Src tyrosine kinases. The Journal of Physical Chemistry. B. 119: 1443-56. PMID 25548962 DOI: 10.1021/Jp511792A  0.3
2015 Jo S, Chipot C, Roux B. Efficient determination of relative entropy using combined temperature and hamiltonian replica-exchange molecular dynamics Journal of Chemical Theory and Computation. 11: 2234-2244. DOI: 10.1021/ct501034w  0.522
2015 Rui H, Das A, Roux B. Na+/K+-ATPase Pumping Mechanism: Insights from Simulations Biophysical Journal. 108: 144a. DOI: 10.1016/J.Bpj.2014.11.796  0.575
2015 Callahan KM, Roux B. Molecular Dynamics Study of Ion Conduction and Selectivity in a Prokaryotic Ion Channel Biophysical Journal. 108: 575a. DOI: 10.1016/J.Bpj.2014.11.3143  0.747
2015 Pond MP, Jo S, Hyde HC, Wright MH, Blachowicz L, Bezanilla F, Roux B. Computational and Experimental Characterization of Intramolecular Regulatory Interactions in Hck Biophysical Journal. 108: 533a. DOI: 10.1016/J.Bpj.2014.11.2923  0.564
2015 Jo S, Jiang W, Roux B. Quantifying Protein-Protein Binding Energy and Entropy using Molecular Dynamics Simulations Biophysical Journal. 108: 41a. DOI: 10.1016/J.Bpj.2014.11.251  0.591
2015 Kazmier K, Sharma S, Islam SM, Roux B, Mchaourab HS. Ligand-Dependent Conformational Cycle of the Na+/Hydantoin Transporter Mhp1 Biophysical Journal. 108: 28a-29a. DOI: 10.1016/J.Bpj.2014.11.181  0.359
2015 DeBerg HA, Islam SM, Puljung MC, Roux B, Zagotta WN, Stoll S. Allosteric Regulation of the Cyclic Nucleotide-Binding Domain in HCN Channels Biophysical Journal. 108: 192a-193a. DOI: 10.1016/J.Bpj.2014.11.1064  0.38
2014 Lin YL, Aleksandrov A, Simonson T, Roux B. An Overview of Electrostatic Free Energy Computations for Solutions and Proteins. Journal of Chemical Theory and Computation. 10: 2690-709. PMID 26586504 DOI: 10.1021/Ct500195P  0.41
2014 McCammon JA, Roux B, Voth G, Yang W. Special Issue on Free Energy. Journal of Chemical Theory and Computation. 10: 2631. PMID 26586502 DOI: 10.1021/Ct500366U  0.426
2014 Jo S, Cheng X, Islam SM, Huang L, Rui H, Zhu A, Lee HS, Qi Y, Han W, Vanommeslaeghe K, MacKerell AD, Roux B, Im W. CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Advances in Protein Chemistry and Structural Biology. 96: 235-65. PMID 25443960 DOI: 10.1016/Bs.Apcsb.2014.06.002  0.745
2014 Kazmier K, Sharma S, Islam SM, Roux B, Mchaourab HS. Conformational cycle and ion-coupling mechanism of the Na+/hydantoin transporter Mhp1. Proceedings of the National Academy of Sciences of the United States of America. 111: 14752-7. PMID 25267652 DOI: 10.1073/Pnas.1410431111  0.367
2014 Huang J, Lopes PE, Roux B, MacKerell AD. Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model. The Journal of Physical Chemistry Letters. 5: 3144-3150. PMID 25247054 DOI: 10.1021/Jz501315H  0.385
2014 Lin YL, Meng Y, Huang L, Roux B. Computational study of Gleevec and G6G reveals molecular determinants of kinase inhibitor selectivity. Journal of the American Chemical Society. 136: 14753-62. PMID 25243930 DOI: 10.1021/Ja504146X  0.334
2014 Chen Y, Roux B. Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal. The Journal of Chemical Physics. 141: 114107. PMID 25240345 DOI: 10.1063/1.4895516  0.335
2014 Jiang W, Phillips JC, Huang L, Fajer M, Meng Y, Gumbart JC, Luo Y, Schulten K, Roux B. Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD. Computer Physics Communications. 185: 908-916. PMID 24944348 DOI: 10.1016/J.Cpc.2013.12.014  0.715
2014 Tempkin JO, Qi B, Saunders MG, Roux B, Dinner AR, Weare J. Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations. The Journal of Chemical Physics. 140: 184114. PMID 24832260 DOI: 10.1063/1.4872021  0.597
2014 Horn R, Roux B, Ã…qvist J. Permeation redux: thermodynamics and kinetics of ion movement through potassium channels. Biophysical Journal. 106: 1859-63. PMID 24806917 DOI: 10.1016/J.Bpj.2014.03.039  0.352
2014 Kazmier K, Sharma S, Quick M, Islam SM, Roux B, Weinstein H, Javitch JA, McHaourab HS. Conformational dynamics of ligand-dependent alternating access in LeuT. Nature Structural & Molecular Biology. 21: 472-9. PMID 24747939 DOI: 10.1038/Nsmb.2816  0.344
2014 Saunders MG, Tempkin J, Weare J, Dinner AR, Roux B, Voth GA. Nucleotide regulation of the structure and dynamics of G-actin. Biophysical Journal. 106: 1710-20. PMID 24739170 DOI: 10.1016/J.Bpj.2014.03.012  0.595
2014 Tietjen GT, Gong Z, Chen CH, Vargas E, Crooks JE, Cao KD, Heffern CT, Henderson JM, Meron M, Lin B, Roux B, Schlossman ML, Steck TL, Lee KY, Adams EJ. Molecular mechanism for differential recognition of membrane phosphatidylserine by the immune regulatory receptor Tim4. Proceedings of the National Academy of Sciences of the United States of America. 111: E1463-72. PMID 24706780 DOI: 10.1016/J.Bpj.2013.11.149  0.346
2014 Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux B. Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model. Plos Computational Biology. 10: e1003521. PMID 24699246 DOI: 10.1371/Journal.Pcbi.1003521  0.61
2014 Binkowski TA, Jiang W, Roux B, Anderson WF, Joachimiak A. Virtual high-throughput ligand screening. Methods in Molecular Biology (Clifton, N.J.). 1140: 251-261. PMID 24590723 DOI: 10.1007/978-1-4939-0354-2_19  0.322
2014 Gumbart JC, Beeby M, Jensen GJ, Roux B. Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations. Plos Computational Biology. 10: e1003475. PMID 24586129 DOI: 10.1371/Journal.Pcbi.1003475  0.595
2014 Shukla D, Meng Y, Roux B, Pande VS. Activation pathway of Src kinase reveals intermediate states as targets for drug design. Nature Communications. 5: 3397. PMID 24584478 DOI: 10.1038/Ncomms4397  0.323
2014 Li Q, Wanderling S, Paduch M, Medovoy D, Singharoy A, McGreevy R, Villalba-Galea CA, Hulse RE, Roux B, Schulten K, Kossiakoff A, Perozo E. Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nature Structural & Molecular Biology. 21: 244-52. PMID 24487958 DOI: 10.1038/Nsmb.2768  0.8
2014 Raghuraman H, Islam SM, Mukherjee S, Roux B, Perozo E. Dynamics transitions at the outer vestibule of the KcsA potassium channel during gating. Proceedings of the National Academy of Sciences of the United States of America. 111: 1831-6. PMID 24429344 DOI: 10.1073/Pnas.1314875111  0.657
2014 Comer J, Roux B, Chipot C. Achieving ergodic sampling using replica-exchange free-energy calculations Molecular Simulation. 40: 218-228. DOI: 10.1080/08927022.2013.841909  0.345
2014 Raghuraman H, Islam SM, Mukherjee S, Roux B, Perozo E. Dynamics transitions at the outer vestibule of the KcsA potassium channel during gating (Proceedings of the National Academy of Sciences of the United States of America (2014) 111, 5 (1831-1836) DOI: 10.1073/pnas.1314875111) Proceedings of the National Academy of Sciences of the United States of America. 111: 4644. DOI: 10.1073/pnas.1402205111  0.542
2014 Qi Y, Cheng X, Han W, Jo S, Roux B, Schulten K, Im W. CHARMM-Gui Pace Cg Builder for Solution, Micelle, Bilayer and Vesicle Simulations Biophysical Journal. 106: 809a. DOI: 10.1016/J.Bpj.2013.11.4437  0.723
2014 Fajer M, Meng Y, Roux B. Simulation of the Conformational Transition Pathway for the Activation of Full-Length C-Src Kinase using the String Method Biophysical Journal. 106: 639a-640a. DOI: 10.1016/J.Bpj.2013.11.3541  0.336
2014 Das A, Roux B. Conformational Transitions in ATP-Driven Calcium Pump SERCA Biophysical Journal. 106: 583a-584a. DOI: 10.1016/J.Bpj.2013.11.3234  0.398
2014 Roux B, Li H, Chowdhary J, Harder E, Lopes PE, Huang L, MacKerell AD. Ion Channel Simulation with Explicit Solvent and Lipid Membrane Based on the Drude Polarizable Force Field Biophysical Journal. 106: 44a. DOI: 10.1016/J.Bpj.2013.11.319  0.484
2014 Lopes PE, Huang J, Shim J, Luo Y, Li H, Savelyev A, Patel D, He X, Roux B, MacKerell AD. Development of a Polarizable Force Field for Macromolecules Based on the Classical Drude Oscillator Biophysical Journal. 106: 43a. DOI: 10.1016/J.Bpj.2013.11.318  0.515
2014 Callahan KM, Roux B. Molecular Dynamics Studies of Ion Conduction in a Prokaryotic Channel Biophysical Journal. 106: 37a. DOI: 10.1016/J.Bpj.2013.11.279  0.75
2014 Jiang W, Phillips J, Huang L, Fajer M, Meng Y, Gumbart JC, luo y, Schulten K, roux b. Generalized Scalable Multiple Copy Algorithms for Biological Molecular Dynamics Simulations in NAMD Biophysical Journal. 106: 412a. DOI: 10.1016/J.Bpj.2013.11.2316  0.716
2014 Shukla D, Roux B, Pande VS. Activation Pathways of Kinases Reveal Intermediate States as Novel Targets for Drug Design Biophysical Journal. 106: 308a. DOI: 10.1016/J.Bpj.2013.11.1784  0.32
2013 Lev B, Roux B, Noskov SY. Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations. Journal of Chemical Theory and Computation. 9: 4165-75. PMID 26592407 DOI: 10.1021/Ct400296W  0.647
2013 Dama JF, Sinitskiy AV, McCullagh M, Weare J, Roux B, Dinner AR, Voth GA. The Theory of Ultra-Coarse-Graining. 1. General Principles. Journal of Chemical Theory and Computation. 9: 2466-80. PMID 26583735 DOI: 10.1021/Ct4000444  0.543
2013 Lopes PE, Huang J, Shim J, Luo Y, Li H, Roux B, Mackerell AD. Force Field for Peptides and Proteins based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. 9: 5430-5449. PMID 24459460 DOI: 10.1021/Ct400781B  0.534
2013 Smith JC, Roux B. Eppur si muove! The 2013 Nobel Prize in Chemistry. Structure (London, England : 1993). 21: 2102-5. PMID 24315458 DOI: 10.1016/J.Str.2013.11.005  0.544
2013 Huang L, Roux B. AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATA. Journal of Chemical Theory and Computation. 9. PMID 24223528 DOI: 10.1021/Ct4003477  0.393
2013 Gumbart JC, Roux B, Chipot C. Efficient determination of protein-protein standard binding free energies from first principles. Journal of Chemical Theory and Computation. 9. PMID 24179453 DOI: 10.1021/Ct400273T  0.625
2013 Dhakshnamoorthy B, Ziervogel BK, Blachowicz L, Roux B. A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations. Journal of the American Chemical Society. 135: 16561-8. PMID 24106986 DOI: 10.1021/Ja407783A  0.824
2013 Khalili-Araghi F, Ziervogel B, Gumbart JC, Roux B. Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations. The Journal of General Physiology. 142: 465-75. PMID 24081985 DOI: 10.1085/Jgp.201311014  0.825
2013 Rowley CN, Roux B. A computational study of barium blockades in the KcsA potassium channel based on multi-ion potential of mean force calculations and free energy perturbation. The Journal of General Physiology. 142: 451-63. PMID 24043859 DOI: 10.1085/Jgp.201311049  0.687
2013 Lin B, Lopes PE, Roux B, MacKerell AD. Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields. The Journal of Chemical Physics. 139: 084509. PMID 24007020 DOI: 10.1063/1.4818731  0.304
2013 Lin YL, Roux B. Computational analysis of the binding specificity of gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinases Journal of the American Chemical Society. 135: 14741-14753. PMID 24001034 DOI: 10.1021/Ja405939X  0.341
2013 Lau AY, Salazar H, Blachowicz L, Ghisi V, Plested AJ, Roux B. A conformational intermediate in glutamate receptor activation. Neuron. 79: 492-503. PMID 23931998 DOI: 10.1016/J.Neuron.2013.06.003  0.549
2013 Venable RM, Luo Y, Gawrisch K, Roux B, Pastor RW. Simulations of anionic lipid membranes: Development of interaction-specific ion parameters and validation using NMR data Journal of Physical Chemistry B. 117: 10183-10192. PMID 23924441 DOI: 10.1021/Jp401512Z  0.515
2013 Ostmeyer J, Chakrapani S, Pan AC, Perozo E, Roux B. Recovery from slow inactivation in K+ channels is controlled by water molecules. Nature. 501: 121-4. PMID 23892782 DOI: 10.1038/Nature12395  0.645
2013 Chowdhary J, Harder E, Lopes PE, Huang L, MacKerell AD, Roux B. A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. The Journal of Physical Chemistry. B. 117: 9142-60. PMID 23841725 DOI: 10.1021/Jp402860E  0.37
2013 Wojtas-Niziurski W, Meng Y, Roux B, Bernèche S. Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions. Journal of Chemical Theory and Computation. 9: 1885-1895. PMID 23814508 DOI: 10.1021/Ct300978B  0.36
2013 Luo Y, Jiang W, Yu H, MacKerell AD, Roux B. Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field. Faraday Discussions. 160: 135-49; discussion 2. PMID 23795497 DOI: 10.1039/C2Fd20068F  0.648
2013 Gumbart JC, Roux B, Chipot C. Standard binding free energies from computer simulations: What is the best strategy? Journal of Chemical Theory and Computation. 9: 794-802. PMID 23794960 DOI: 10.1021/Ct3008099  0.61
2013 Beeby M, Gumbart JC, Roux B, Jensen GJ. Architecture and assembly of the Gram-positive cell wall. Molecular Microbiology. 88: 664-72. PMID 23600697 DOI: 10.1111/Mmi.12203  0.552
2013 Islam SM, Stein RA, McHaourab HS, Roux B. Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme. The Journal of Physical Chemistry. B. 117: 4740-54. PMID 23510103 DOI: 10.1021/Jp311723A  0.328
2013 Roux B, Weare J. On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method Journal of Chemical Physics. 138. PMID 23464140 DOI: 10.1063/1.4792208  0.355
2013 Yu W, Lopes PE, Roux B, MacKerell AD. Six-site polarizable model of water based on the classical Drude oscillator. The Journal of Chemical Physics. 138: 034508. PMID 23343286 DOI: 10.1063/1.4774577  0.314
2013 Lin YL, Meng Y, Jiang W, Roux B. Explaining why Gleevec is a specific and potent inhibitor of Abl kinase Proceedings of the National Academy of Sciences of the United States of America. 110: 1664-1669. PMID 23319661 DOI: 10.1073/Pnas.1214330110  0.352
2013 Gumbart JC, Teo I, Roux B, Schulten K. Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion. Journal of the American Chemical Society. 135: 2291-7. PMID 23298280 DOI: 10.1016/J.Bpj.2012.11.2274  0.707
2013 Jo S, Jiang W, Lee HS, Roux B, Im W. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application. Journal of Chemical Information and Modeling. 53: 267-77. PMID 23205773 DOI: 10.1021/Ci300505N  0.676
2013 Ziervogel BK, Roux B. The binding of antibiotics in OmpF porin. Structure (London, England : 1993). 21: 76-87. PMID 23201272 DOI: 10.1016/J.Str.2012.10.014  0.813
2013 Riahi S, Roux B, Rowley CN. QM/MM molecular dynamics simulations of the hydration of Mg(II) and Zn(II) ions Canadian Journal of Chemistry. 91: 552-558. DOI: 10.1139/cjc-2012-0515  0.614
2013 Lev B, Roux B, Noskov SY. Relative free energies for hydration of monovalent ions from QM and QM/MM simulations Journal of Chemical Theory and Computation. 9: 4165-4175. DOI: 10.1021/ct400296w  0.551
2013 Dama JF, Sinitskiy AV, McCullagh M, Weare J, Roux B, Dinner AR, Voth GA. The theory of ultra-coarse-graining. 1. General principles Journal of Chemical Theory and Computation. 9: 2466-2480. DOI: 10.1021/ct4000444  0.456
2013 Callahan KM, Roux B. Computational Study of the Prokaryotic Sodium Channel Biophysical Journal. 104: 136a. DOI: 10.1016/J.Bpj.2012.11.776  0.749
2013 Medovoy D, Li Q, Perozo E, Roux B. The Energetic Landscape of the Putative Voltage-Driven Conformational Transition in Ci-VSP Biophysical Journal. 104: 124a. DOI: 10.1016/J.Bpj.2012.11.714  0.803
2013 Gumbart JC, Beeby M, Jensen G, Roux B. Assembly and Architecture of Gram-Positive and -Negative Cell Walls Biophysical Journal. 104: 642a. DOI: 10.1016/J.Bpj.2012.11.3544  0.592
2013 Li H, Callahan K, Mackerell AD, Roux B. Development of the Charmm Drude Polarizable Force Field for the Study of Ion Interactions in Biological Systems Biophysical Journal. 104: 507a. DOI: 10.1016/J.Bpj.2012.11.2799  0.752
2013 Das A, Gur M, Bahar I, Roux B. A Simple Coarse-Grained Model to Map the Transition Pathway Between Two Stable Conformations using the Anisotropic Elastic Network Model Biophysical Journal. 104: 35a-36a. DOI: 10.1016/J.Bpj.2012.11.235  0.344
2013 Chowdhary J, Li H, Harder E, Lopes P, MacKerell A, Roux B. Drude Model Based Polarizable Force Field for Lipids Biophysical Journal. 104: 31a. DOI: 10.1016/J.Bpj.2012.11.210  0.371
2013 Tietjen GT, Chen C, Crooks J, Vargas E, Cao K, Heffern C, Lin B, Meron M, Roux B, Schlossman M, Adams E, Yee Lee K. Elucidating the Molecular Details of Phosphatidylserine Membrane Recognition in Immune Response Biophysical Journal. 104: 363a. DOI: 10.1016/J.Bpj.2012.11.2016  0.334
2013 Islam SM, Stein R, Mchaourab H, Roux B. Rotamer Library of Spin Labeled Cysteines Attached to T4 Lysozyme Deduced from Molecular Dynamics Simulations Constrained by Double Electron-Electron Resonance (Deer) Experiments Biophysical Journal. 104: 335a. DOI: 10.1016/J.Bpj.2012.11.1862  0.337
2013 Ostmeyer JL, Chakrapani S, Perozo E, Roux B. Rate of Recovery from Slow Inactivation in K+ Channels Controlled by Buried Water Molecules Biophysical Journal. 104: 25a-26a. DOI: 10.1016/J.Bpj.2012.11.174  0.595
2013 Sánchez-Rodríguez JE, Khalili-Araghi F, Adhikari A, Sosnick T, Roux B, Holmgren M, Bezanilla F. Probing Conformational Changes of the Na+/K+ ATPase upon Ouabain Binding by using a Spectroscopic Approach Biophysical Journal. 104: 300a. DOI: 10.1016/J.Bpj.2012.11.1669  0.583
2013 Dhakshnamoorthy B, Blachowicz L, Roux B. Permeation Pathways of Cations and Anions in the OmpF Porin Channel using Anomalous X-Ray Scattering Biophysical Journal. 104: 183a. DOI: 10.1016/J.Bpj.2012.11.1030  0.406
2012 Jiang W, Luo Y, Maragliano L, Roux B. Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer. Journal of Chemical Theory and Computation. 8: 4672-4680. PMID 26605623 DOI: 10.1021/Ct300468G  0.53
2012 Rowley CN, Roux B. The Solvation Structure of Na(+) and K(+) in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 8: 3526-3535. PMID 26593000 DOI: 10.1021/Ct300091W  0.704
2012 Lacroix JJ, Pless SA, Maragliano L, Campos FV, Galpin JD, Ahern CA, Roux B, Bezanilla F. Intermediate state trapping of a voltage sensor. The Journal of General Physiology. 140: 635-52. PMID 23183699 DOI: 10.1085/Jgp.201210827  0.391
2012 Vargas E, Yarov-Yarovoy V, Khalili-Araghi F, Catterall WA, Klein ML, Tarek M, Lindahl E, Schulten K, Perozo E, Bezanilla F, Roux B. An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations. The Journal of General Physiology. 140: 587-94. PMID 23183694 DOI: 10.1085/Jgp.201210873  0.711
2012 Hyde HC, Sandtner W, Vargas E, Dagcan AT, Robertson JL, Roux B, Correa AM, Bezanilla F. Nano-positioning system for structural analysis of functional homomeric proteins in multiple conformations. Structure (London, England : 1993). 20: 1629-40. PMID 23063010 DOI: 10.1016/J.Str.2012.08.022  0.585
2012 Robertson JL, Palmer LG, Roux B. Multi-ion distributions in the cytoplasmic domain of inward rectifier potassium channels. Biophysical Journal. 103: 434-43. PMID 22947859 DOI: 10.1016/J.Bpj.2012.06.023  0.718
2012 Raghuraman H, Cordero-Morales JF, Jogini V, Pan AC, Kollewe A, Roux B, Perozo E. Mechanism of Cd2+ coordination during slow inactivation in potassium channels. Structure (London, England : 1993). 20: 1332-42. PMID 22771214 DOI: 10.1016/J.Str.2012.03.027  0.607
2012 Herrou J, Rotskoff G, Luo Y, Roux B, Crosson S. Structural basis of a protein partner switch that regulates the general stress response of α-proteobacteria. Proceedings of the National Academy of Sciences of the United States of America. 109: E1415-23. PMID 22550172 DOI: 10.1073/Pnas.1116887109  0.471
2012 Roux B. Ion binding sites and their representations by reduced models. The Journal of Physical Chemistry. B. 116: 6966-79. PMID 22494321 DOI: 10.1021/Jp3007365  0.377
2012 Roux B. Comment on "Probing the thermodynamics of competitive ion binding using minimum energy structures". The Journal of Physical Chemistry. B. 116: 7991-3. PMID 22475045 DOI: 10.1021/Jp207032P  0.429
2012 Kwon T, Roux B, Jo S, Klauda JB, Harris AL, Bargiello TA. Molecular dynamics simulations of the Cx26 hemichannel: insights into voltage-dependent loop-gating. Biophysical Journal. 102: 1341-51. PMID 22455917 DOI: 10.1016/J.Bpj.2012.02.009  0.614
2012 Gumbart J, Roux B. Determination of membrane-insertion free energies by molecular dynamics simulations. Biophysical Journal. 102: 795-801. PMID 22385850 DOI: 10.1016/J.Bpj.2012.01.021  0.629
2012 Khalili-Araghi F, Tajkhorshid E, Roux B, Schulten K. Molecular dynamics investigation of the ω-current in the Kv1.2 voltage sensor domains. Biophysical Journal. 102: 258-67. PMID 22339862 DOI: 10.1016/J.Bpj.2011.10.057  0.558
2012 Lee KI, Jo S, Rui H, Egwolf B, Roux B, Pastor RW, Im W. Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores. Journal of Computational Chemistry. 33: 331-9. PMID 22102176 DOI: 10.1002/Jcc.21952  0.774
2012 Gumbart J, Khalili-Araghi F, Sotomayor M, Roux B. Constant electric field simulations of the membrane potential illustrated with simple systems. Biochimica Et Biophysica Acta. 1818: 294-302. PMID 22001851 DOI: 10.1016/J.Bbamem.2011.09.030  0.618
2012 Khalili-Araghi F, Ziervogel B, Roux B, Gumbart J. Membrane protein simulations under asymmetric ionic concentrations Acm International Conference Proceeding Series. DOI: 10.1145/2335755.2335812  0.788
2012 Yu H, Ratheal I, Artigas P, Roux B. Molecular mechanisms of K + selectivity in Na/K pump Australian Journal of Chemistry. 65: 448-456. DOI: 10.1071/Ch12026  0.533
2012 Rowley CN, Roux B. The solvation structure of Na + and K + in liquid water determined from high level ab initio molecular dynamics simulations Journal of Chemical Theory and Computation. 8: 3526-3535. DOI: 10.1021/ct300091w  0.637
2012 Sanchez-Rodriguez JE, Khalili-Araghi F, Roux B, Holmgren M, Bezanilla F. Changes of Intramolecular Distances in the Na+/K+ Atpase upon Ouabain Binding Biophysical Journal. 102: 708a. DOI: 10.1016/J.Bpj.2011.11.3843  0.335
2012 Medovoy D, Cuello LCG, Perozo E, Roux B. A Three-Ion Selectivity Filter Potential Energy Landscape of a Putative Open-Conductive KcsA Biophysical Journal. 102: 676a-677a. DOI: 10.1016/J.Bpj.2011.11.3680  0.824
2012 Salazar Garcia HP, Lau AY, Blachowicz L, Plested AJ, Roux B. Interdimer Contacts Paint a New Picture of Glutamate Receptor Activation Biophysical Journal. 102: 612a. DOI: 10.1016/J.Bpj.2011.11.3339  0.553
2012 Sandtner W, Egwolf B, Khalili-Araghi F, Sanchez-Rodríguez JE, Roux B, Bezanilla F, Holmgren M. Ouabain Binding Site in a Functioning Na+/K+-ATPase Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.3306  0.353
2012 Lacroix JJ, Pless SA, Campos FV, Maragliano L, Galpin JD, Ahern CA, Roux B, Bezanilla F. Position of the Second Gating Charge along S4 in an Intermediate Conformation of a K+ Channel Voltage Sensor Biophysical Journal. 102: 530a. DOI: 10.1016/J.Bpj.2011.11.2899  0.383
2012 Gumbart JC, Roux B, Schulten K. Spontaneous Movement of Transmembrane Segments from SecY into the Membrane Biophysical Journal. 102: 431a. DOI: 10.1016/J.Bpj.2011.11.2359  0.687
2012 Rowley CN, Roux B. Interpreting the Barium Blockades of Potassium Channels with the Multi-Ion Permeation Free Energy Surface Biophysical Journal. 102: 333a. DOI: 10.1016/J.Bpj.2011.11.1827  0.697
2012 Roux B, Noskov SY. Corrigendum for Biophysical Chemistry 124 (2006) 279–291 Biophysical Chemistry. 161: 54. DOI: 10.1016/J.Bpc.2011.10.004  0.488
2011 Vargas E, Bezanilla F, Roux B. In search of a consensus model of the resting state of a voltage-sensing domain. Neuron. 72: 713-20. PMID 22153369 DOI: 10.1016/J.Neuron.2011.09.024  0.378
2011 Pan AC, Cuello LG, Perozo E, Roux B. Thermodynamic coupling between activation and inactivation gating in potassium channels revealed by free energy molecular dynamics simulations. The Journal of General Physiology. 138: 571-80. PMID 22124115 DOI: 10.1085/Jgp.201110670  0.66
2011 Sandtner W, Egwolf B, Khalili-Araghi F, Sánchez-Rodríguez JE, Roux B, Bezanilla F, Holmgren M. Ouabain binding site in a functioning Na+/K+ ATPase. The Journal of Biological Chemistry. 286: 38177-83. PMID 21911500 DOI: 10.1074/Jbc.M111.267682  0.341
2011 Yu H, Ratheal IM, Artigas P, Roux B. Protonation of key acidic residues is critical for the K⁺-selectivity of the Na/K pump. Nature Structural & Molecular Biology. 18: 1159-63. PMID 21909093 DOI: 10.1038/Nsmb.2113  0.531
2011 Roux B. Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail. Biophysical Journal. 101: 755-6. PMID 21843464 DOI: 10.1016/J.Bpj.2011.07.002  0.412
2011 Ingólfsson HI, Li Y, Vostrikov VV, Gu H, Hinton JF, Koeppe RE, Roux B, Andersen OS. Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. I: molecular dynamics simulations. The Journal of Physical Chemistry. B. 115: 7417-26. PMID 21574563 DOI: 10.1021/Jp200904D  0.438
2011 Vostrikov VV, Gu H, Ingólfsson HI, Hinton JF, Andersen OS, Roux B, Koeppe RE. Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. II: nuclear magnetic resonance experiments. The Journal of Physical Chemistry. B. 115: 7427-32. PMID 21574558 DOI: 10.1021/Jp200906Y  0.366
2011 Jiang W, Hardy DJ, Phillips JC, Mackerell AD, Schulten K, Roux B. High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. The Journal of Physical Chemistry Letters. 2: 87-92. PMID 21572567 DOI: 10.1021/Jz101461D  0.525
2011 Roux B, Bernèche S, Egwolf B, Lev B, Noskov SY, Rowley CN, Yu H. Ion selectivity in channels and transporters. The Journal of General Physiology. 137: 415-26. PMID 21518830 DOI: 10.1085/Jgp.201010577  0.771
2011 Lau AY, Roux B. Structural biology: One domain, multiple conformations. Nature Chemical Biology. 7: 130-1. PMID 21321548 DOI: 10.1038/Nchembio.527  0.577
2011 Lau AY, Roux B. The hidden energetics of ligand binding and activation in a glutamate receptor. Nature Structural & Molecular Biology. 18: 283-7. PMID 21317895 DOI: 10.1016/J.Bpj.2010.12.1675  0.567
2011 Gajewski C, Dagcan A, Roux B, Deutsch C. Biogenesis of the pore architecture of a voltage-gated potassium channel. Proceedings of the National Academy of Sciences of the United States of America. 108: 3240-5. PMID 21300900 DOI: 10.1073/Pnas.1017097108  0.411
2011 Yang S, Roux B. EROS: Better than SAXS! Structure (London, England : 1993). 19: 3-4. PMID 21220109 DOI: 10.1016/J.Str.2010.12.008  0.686
2011 Chakrapani S, Cordero-Morales JF, Jogini V, Pan AC, Cortes DM, Roux B, Perozo E. On the structural basis of modal gating behavior in K(+) channels. Nature Structural & Molecular Biology. 18: 67-74. PMID 21186363 DOI: 10.1038/Nsmb.1968  0.613
2011 Luo Y, Harder E, Faibish RS, Roux B. Computer simulations of water flux and salt permeability of the reverse osmosis FT-30 aromatic polyamide membrane Journal of Membrane Science. 384: 1-9. DOI: 10.1016/J.Memsci.2011.08.057  0.523
2011 Lopes PE, Zhu X, Lau A, Roux B, MacKerell AD. Development of the Charmm Polarizable Force Field for Polypeptides Based on Drude Oscillators Biophysical Journal. 100: 612a. DOI: 10.1016/J.Bpj.2010.12.3527  0.559
2011 Cordero-Morales JF, Jogini V, Vasquez V, Bourdeau RW, Yu H, Roux B, Tristani-Firouzi M, Perozo E. Engineering the hERG1 Selectivity Filter into the NaK Pore Domain Biophysical Journal. 100: 584a. DOI: 10.1016/J.Bpj.2010.12.3372  0.676
2011 Rowley CN, Lev B, Noskov S, Roux B. QM/MM Modeling of Ba2+ Blockades in Potassium ion Channels Biophysical Journal. 100: 565a. DOI: 10.1016/J.Bpj.2010.12.3280  0.758
2011 Vargas E, Bezanilla F, Roux B. A Converging Consensus of the Structure of a Voltage-Sensing Domain in its Resting State Biophysical Journal. 100: 367a. DOI: 10.1016/J.Bpj.2010.12.2193  0.399
2011 Maragliano L, Khalili-Araghi F, Tajkhorshid E, Schulten K, Roux B. The Conformational Transition of Kv1.2 Voltage Sensor Domain from Molecular Dynamics Simulations Biophysical Journal. 100: 284a-285a. DOI: 10.1016/J.Bpj.2010.12.1760  0.565
2011 Ziervogel B, Dhaksnamoorthy B, Blachowicz L, Roux B. Antibiotic Binding and Dynamics within the OmpF Channel Allow Transfer Across the Bacterial Outer Membrane Biophysical Journal. 100: 244a. DOI: 10.1016/J.Bpj.2010.12.1550  0.82
2010 Jiang W, Roux B. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. Journal of Chemical Theory and Computation. 6: 2559-2565. PMID 21857813 DOI: 10.1021/Ct1001768  0.4
2010 Yu H, Noskov SY, Roux B. Two mechanisms of ion selectivity in protein binding sites. Proceedings of the National Academy of Sciences of the United States of America. 107: 20329-34. PMID 21057111 DOI: 10.1073/Pnas.1007150107  0.678
2010 Contreras JE, Chen J, Lau AY, Jogini V, Roux B, Holmgren M. Voltage profile along the permeation pathway of an open channel. Biophysical Journal. 99: 2863-9. PMID 21044583 DOI: 10.1016/J.Bpj.2010.08.053  0.602
2010 Li Y, Andersen OS, Roux B. Energetics of double-ion occupancy in the gramicidin A channel. The Journal of Physical Chemistry. B. 114: 13881-8. PMID 20939567 DOI: 10.1021/Jp105820U  0.4
2010 Ratheal IM, Virgin GK, Yu H, Roux B, Gatto C, Artigas P. Selectivity of externally facing ion-binding sites in the Na/K pump to alkali metals and organic cations. Proceedings of the National Academy of Sciences of the United States of America. 107: 18718-23. PMID 20937860 DOI: 10.1073/Pnas.1004214107  0.533
2010 Yang S, Blachowicz L, Makowski L, Roux B. Multidomain assembled states of Hck tyrosine kinase in solution. Proceedings of the National Academy of Sciences of the United States of America. 107: 15757-62. PMID 20798061 DOI: 10.1073/Pnas.1004569107  0.683
2010 Yang S, Parisien M, Major F, Roux B. RNA structure determination using SAXS data. The Journal of Physical Chemistry. B. 114: 10039-48. PMID 20684627 DOI: 10.1021/Jp1057308  0.662
2010 Yu H, Mazzanti CL, Whitfield TW, Koeppe RE, Andersen OS, Roux B. A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide. Journal of the American Chemical Society. 132: 10847-56. PMID 20681718 DOI: 10.1021/Ja103270W  0.617
2010 Dalmas O, Cuello LG, Jogini V, Cortes DM, Roux B, Perozo E. Structural dynamics of the magnesium-bound conformation of CorA in a lipid bilayer. Structure (London, England : 1993). 18: 868-78. PMID 20637423 DOI: 10.1016/J.Str.2010.04.009  0.619
2010 Egwolf B, Roux B. Ion selectivity of the KcsA channel: a perspective from multi-ion free energy landscapes. Journal of Molecular Biology. 401: 831-42. PMID 20624398 DOI: 10.1016/J.Jmb.2010.07.006  0.423
2010 Cuello LG, Jogini V, Cortes DM, Pan AC, Gagnon DG, Dalmas O, Cordero-Morales JF, Chakrapani S, Roux B, Perozo E. Structural basis for the coupling between activation and inactivation gates in K(+) channels. Nature. 466: 272-5. PMID 20613845 DOI: 10.1038/Nature09136  0.643
2010 Ge X, Roux B. Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome. The Journal of Physical Chemistry. B. 114: 9525-39. PMID 20608691 DOI: 10.1021/Jp100579Y  0.393
2010 Roux B, Yu H. Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory. The Journal of Chemical Physics. 132: 234101. PMID 20572683 DOI: 10.1063/1.3436632  0.586
2010 Roux B. Exploring the ion selectivity properties of a large number of simplified binding site models. Biophysical Journal. 98: 2877-85. PMID 20550900 DOI: 10.1016/J.Bpj.2010.03.038  0.398
2010 Roux B. Perspectives on: molecular dynamics and computational methods. The Journal of General Physiology. 135: 547-8. PMID 20513755 DOI: 10.1083/Jcb1896Oia16  0.311
2010 Khalili-Araghi F, Jogini V, Yarov-Yarovoy V, Tajkhorshid E, Roux B, Schulten K. Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Biophysical Journal. 98: 2189-98. PMID 20483327 DOI: 10.1016/J.Bpj.2010.02.056  0.575
2010 Baker CM, Lopes PE, Zhu X, Roux B, Mackerell AD. Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. Journal of Chemical Theory and Computation. 6: 1181-1198. PMID 20401166 DOI: 10.1021/Ct9005773  0.346
2010 Yu H, Whitfield TW, Harder E, Lamoureux G, Vorobyov I, Anisimov VM, Mackerell AD, Roux B. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. Journal of Chemical Theory and Computation. 6: 774-786. PMID 20300554 DOI: 10.1021/Ct900576A  0.687
2010 Chakrapani S, Sompornpisut P, Intharathep P, Roux B, Perozo E. The activated state of a sodium channel voltage sensor in a membrane environment. Proceedings of the National Academy of Sciences of the United States of America. 107: 5435-40. PMID 20207950 DOI: 10.1073/Pnas.0914109107  0.654
2010 Ge X, Roux B. Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials. Journal of Molecular Recognition : Jmr. 23: 128-41. PMID 20151411 DOI: 10.1002/Jmr.996  0.406
2010 Egwolf B, Luo Y, Walters DE, Roux B. Ion selectivity of alpha-hemolysin with beta-cyclodextrin adapter. II. Multi-ion effects studied with grand canonical Monte Carlo/Brownian dynamics simulations. The Journal of Physical Chemistry. B. 114: 2901-9. PMID 20146515 DOI: 10.1021/Jp906791B  0.534
2010 Luo Y, Egwolf B, Walters DE, Roux B. Ion selectivity of alpha-hemolysin with a beta-cyclodextrin adapter. I. Single ion potential of mean force and diffusion coefficient. The Journal of Physical Chemistry. B. 114: 952-8. PMID 20041673 DOI: 10.1021/Jp906790F  0.559
2010 Dhakshnamoorthy B, Raychaudhury S, Blachowicz L, Roux B. Cation-selective pathway of OmpF porin revealed by anomalous X-ray diffraction. Journal of Molecular Biology. 396: 293-300. PMID 19932117 DOI: 10.1016/J.Jmb.2009.11.042  0.346
2010 Truchon JF, Nicholl's A, Grant JA, Iftimie RI, Roux B, Bayly CI. Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions. Journal of Computational Chemistry. 31: 811-24. PMID 19598266 DOI: 10.1002/Jcc.21369  0.349
2010 Roux B. Proton wires are different. Biophysical Journal. 77: 2331-2. PMID 10545337 DOI: 10.1016/S0006-3495(99)77071-2  0.349
2010 Luo Y, Roux B. Simulation of osmotic pressure in concentrated aqueous salt solutions Journal of Physical Chemistry Letters. 1: 183-189. DOI: 10.1021/Jz900079W  0.503
2010 Yang S, Blachowicz L, Makowski L, Roux B. Small-Angle X-Ray Scattering and Computational Modeling Reveal the Multi-Domain Assembly States of Hck in Solution Biophysical Journal. 98: 177a. DOI: 10.1016/J.Bpj.2009.12.944  0.682
2010 Virgin G, Ratheal I, Yaragatupalli S, Yu H, Roux B, Gatto C, Artigas P. Ion-Selectivity of Externally Facing Na+-Exclusive and Na+/K+-Shared Sites in the Na/K-Pump Biophysical Journal. 98: 168a. DOI: 10.1016/J.Bpj.2009.12.909  0.502
2010 Gajewski C, Dagcan A, Pian T, Roux B, Deutsch C. Biogenesis of Pore Architecture in Voltage-Gated K+ Channels Biophysical Journal. 98: 117a. DOI: 10.1016/J.Bpj.2009.12.637  0.407
2010 Ziervogel B, Dhakshnamoorthy B, Blachowicz L, Roux B. The Role of Microscopic Interactions for Effective Antibiotic Delivery across the Bacterial Outer Membrane Biophysical Journal. 98: 683a-684a. DOI: 10.1016/J.Bpj.2009.12.3755  0.795
2010 Vargas E, Villalba-Galea CA, Roux B, Bezanilla F. Structural Model of the Voltage Sensing Domain in Ci-VSP Biophysical Journal. 98: 645a. DOI: 10.1016/J.Bpj.2009.12.3533  0.405
2010 Pan AC, Chakrapani S, Jogini V, Cuello LG, Cortes DM, Perozo E, Roux B. The Importance of Ion Binding for Potassium Channel Inactivation and Recovery Biophysical Journal. 98: 621a. DOI: 10.1016/J.Bpj.2009.12.3400  0.647
2010 Lau AY, Roux B. The Free Energies of Ligand-Binding to the Ionotropic Glutamate Receptor Biophysical Journal. 98: 609a-610a. DOI: 10.1016/J.Bpj.2009.12.3324  0.572
2010 Hyde HC, Sandtner W, Robertson J, Dagcan A, Roux B, Bezanilla F, Correa AM. 3D Geometric Monte Carlo Fitting of LRET Data Biophysical Journal. 98: 521a. DOI: 10.1016/J.Bpj.2009.12.2832  0.597
2010 Maragliano L, Khalili-Araghi F, Tajkhorshid E, Schulten K, Roux B. Pathway Calculation of the Conformational Transition of the Voltage Sensor Domain in the Kv1.2 Channel Biophysical Journal. 98: 521a. DOI: 10.1016/J.Bpj.2009.12.2831  0.563
2010 Khalili-Araghi F, Jogini V, Yarov-Yarovoy V, Tajkhorshid E, Roux B, Schulten K. Refinement and Validation of Atomic Models of the Kv1.2 Potassium Channel Through Molecular Dynamics and Gating Charge Calculations Biophysical Journal. 98: 520a-521a. DOI: 10.1016/J.Bpj.2009.12.2830  0.582
2010 Li Y, Andersen OS, Roux B. Mechanisms of Ion Permeation through Gramicidin a Channels Biophysical Journal. 98: 330a. DOI: 10.1016/J.Bpj.2009.12.1791  0.425
2010 Yu H, Noskov SY, Roux B. The Role of Architectural and Structural Forces in Ion Selectivity Biophysical Journal. 98: 330a. DOI: 10.1016/J.Bpj.2009.12.1790  0.68
2010 Yu H, Artigas P, Roux B. Microscopic Mechanism of Ion Selectivity in the Nak Pump Biophysical Journal. 98: 330a. DOI: 10.1016/J.Bpj.2009.12.1789  0.557
2010 Gan W, Roux B. Characterization of Conformational Transitions in Src Kinase using the String Method with Swarms-of-Trajectories and Markovian Milestoning Biophysical Journal. 98: 232a. DOI: 10.1016/J.Bpj.2009.12.1256  0.584
2010 Harder E, Roux B, MacKerell AD. Molecular Dynamics Simulation of Phospholipid Bilayers and Monolayers Using a Polarizable Force Field Biophysical Journal. 98: 10a. DOI: 10.1016/J.Bpj.2009.12.061  0.359
2009 Shivakumar D, Deng Y, Roux B. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model. Journal of Chemical Theory and Computation. 5: 919-30. PMID 26609601 DOI: 10.1021/Ct800445X  0.81
2009 Truchon JF, Nicholls A, Roux B, Iftimie RI, Bayly CI. Integrated Continuum Dielectric Approaches to treat Molecular Polarizability and the Condensed Phase: Refractive Index and Implicit Solvation. Journal of Chemical Theory and Computation. 5: 1785-1802. PMID 24826083 DOI: 10.1021/Ct900029D  0.309
2009 Jiang W, Hodoscek M, Roux B. Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD). Journal of Chemical Theory and Computation. 5: 2583-2588. PMID 21857812 DOI: 10.1021/Ct900223Z  0.386
2009 Lopes PE, Roux B, Mackerell AD. Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications. Theoretical Chemistry Accounts. 124: 11-28. PMID 20577578 DOI: 10.1007/S00214-009-0617-X  0.366
2009 Maragliano L, Vanden-Eijnden E, Roux B. Free energy and kinetics of conformational transitions from Voronoi tessellated milestoning with restraining potentials. Journal of Chemical Theory and Computation. 5: 2589-2594. PMID 20354583 DOI: 10.1021/Ct900279Z  0.356
2009 Yu H, Roux B. On the utilization of energy minimization to the study of ion selectivity. Biophysical Journal. 97: L15-7. PMID 19843443 DOI: 10.1016/J.Bpj.2009.08.005  0.553
2009 Gan W, Yang S, Roux B. Atomistic view of the conformational activation of Src kinase using the string method with swarms-of-trajectories. Biophysical Journal. 97: L8-L10. PMID 19686639 DOI: 10.1016/J.Bpj.2009.06.016  0.762
2009 Tan K, Sather A, Robertson JL, Moy S, Roux B, Joachimiak A. Structure and electrostatic property of cytoplasmic domain of ZntB transporter. Protein Science : a Publication of the Protein Society. 18: 2043-52. PMID 19653298 DOI: 10.1002/Pro.215  0.565
2009 Harder E, Walters DE, Bodnar YD, Faibish RS, Roux B. Molecular dynamics study of a polymeric reverse osmosis membrane. The Journal of Physical Chemistry. B. 113: 10177-82. PMID 19586002 DOI: 10.1021/Jp902715F  0.367
2009 Kollewe A, Lau AY, Sullivan A, Roux B, Goldstein SA. A structural model for K2P potassium channels based on 23 pairs of interacting sites and continuum electrostatics. The Journal of General Physiology. 134: 53-68. PMID 19564427 DOI: 10.1085/Jgp.200910235  0.566
2009 Yu H, Noskov SY, Roux B. Hydration number, topological control, and ion selectivity. The Journal of Physical Chemistry. B. 113: 8725-30. PMID 19489546 DOI: 10.1021/Jp901233V  0.68
2009 Yang S, Park S, Makowski L, Roux B. A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes. Biophysical Journal. 96: 4449-63. PMID 19486669 DOI: 10.1016/J.Bpj.2009.03.036  0.689
2009 Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, et al. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry. 30: 1545-614. PMID 19444816 DOI: 10.1002/Jcc.21287  0.794
2009 Freddolino PL, Park S, Roux B, Schulten K. Force field bias in protein folding simulations. Biophysical Journal. 96: 3772-80. PMID 19413983 DOI: 10.1016/J.Bpj.2009.02.033  0.522
2009 Park S, Bardhan JP, Roux B, Makowski L. Simulated x-ray scattering of protein solutions using explicit-solvent models. The Journal of Chemical Physics. 130: 134114. PMID 19355724 DOI: 10.1063/1.3099611  0.306
2009 Numano R, Szobota S, Lau AY, Gorostiza P, Volgraf M, Roux B, Trauner D, Isacoff EY. Nanosculpting reversed wavelength sensitivity into a photoswitchable iGluR. Proceedings of the National Academy of Sciences of the United States of America. 106: 6814-9. PMID 19342491 DOI: 10.1016/J.Neures.2010.07.2065  0.56
2009 Yang S, Banavali NK, Roux B. Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Proceedings of the National Academy of Sciences of the United States of America. 106: 3776-81. PMID 19225111 DOI: 10.1073/Pnas.0808261106  0.7
2009 Harder E, Mackerell AD, Roux B. Many-body polarization effects and the membrane dipole potential. Journal of the American Chemical Society. 131: 2760-1. PMID 19199514 DOI: 10.1021/Ja806825G  0.336
2009 Sezer D, Freed JH, Roux B. Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations. Journal of the American Chemical Society. 131: 2597-605. PMID 19191603 DOI: 10.1021/Ja8073819  0.313
2009 Deng Y, Roux B. Computations of standard binding free energies with molecular dynamics simulations. The Journal of Physical Chemistry. B. 113: 2234-46. PMID 19146384 DOI: 10.1021/Jp807701H  0.406
2009 Harder E, Roux B. On the origin of the electrostatic potential difference at a liquid-vacuum interface. The Journal of Chemical Physics. 129: 234706. PMID 19102551 DOI: 10.1063/1.3027513  0.37
2009 Gan W, Roux B. Binding specificity of SH2 domains: insight from free energy simulations. Proteins. 74: 996-1007. PMID 18767163 DOI: 10.1002/Prot.22209  0.574
2009 Banavali NK, Roux B. Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases. Proteins. 74: 378-89. PMID 18623061 DOI: 10.1002/Prot.22153  0.323
2009 Khalili-Araghi F, Jogini V, Yarov-Yarovoy V, Tajkhorshid E, Roux B, Schulten K. Molecular Dynamics Simulation of the Kv1.2 Potassium Channel Biophysical Journal. 96: 191a-192a. DOI: 10.1016/J.Bpj.2008.12.899  0.572
2009 Ingolfsson HI, Vostrikov VV, Gu H, Koeppe RE, Hinton JF, Roux B, Allen TW, Andersen OS. Evaluating Gramicidin A Channel Backbone Dynamics by Molecular Dynamics and Nuclear Magnetic Resonance Biophysical Journal. 96: 152a-153a. DOI: 10.1016/J.Bpj.2008.12.688  0.624
2009 Kondrashov DA, Pan AC, Roux B. Transition Pathway Calculation Using Interpolated Parameters From Swarms Of Trajectories Biophysical Journal. 96: 573a. DOI: 10.1016/J.Bpj.2008.12.3751  0.331
2009 Egwolf B, Luo Y, Walters DE, Roux B. Computational Study on the Ion Selectivity of Modified Alpha-Hemolysin Channels Biophysical Journal. 96: 662a. DOI: 10.1016/J.Bpj.2008.12.3499  0.572
2009 Yu H, Whitfield TW, Noskov SY, Mazzanti CL, Koeppe RE, Andersen OS, Roux B. Development of a Drude Polarizable Force Field for Ion-water and Ion-NMA Interactions and Application to Selectivity in Ion Channels Biophysical Journal. 96: 660a. DOI: 10.1016/J.Bpj.2008.12.3488  0.693
2009 Pan AC, Jogini V, Cuello LG, Cortes D, Perozo E, Roux B. Free Energy Landscape for the Inactivation of the KcsA Potassium Channel Biophysical Journal. 96: 657a. DOI: 10.1016/J.Bpj.2008.12.3469  0.651
2009 Ge X, Roux B. Free Energy Calculations of Sparsomycin Analogs Binding to the Ribosome with Molecular Dynamics Simulations Biophysical Journal. 96: 83a. DOI: 10.1016/J.Bpj.2008.12.333  0.4
2009 Gan W, Roux B. Folding Pathway And Free Energy Landscape Of Villin Headpiece Subdomain HP35 Studied by String Method Biophysical Journal. 96: 590a-591a. DOI: 10.1016/J.Bpj.2008.12.3093  0.572
2009 Cuello LG, Jogini V, Cortes DM, Pan AC, Gagnon DG, Cordero-Morales JF, Chakrapani S, Roux B, Perozo E. Structural Basis For The Coupling Between Activation And Inactivation Gating In Potassium Channels Biophysical Journal. 96: 381a. DOI: 10.1016/J.Bpj.2008.12.2852  0.637
2009 Robertson JL, Palmer LG, Roux B. The Behavior of Ions Inside the Cytoplasmic Domain of Inward Rectifier Potassium Channels Biophysical Journal. 96: 463a. DOI: 10.1016/J.Bpj.2008.12.2383  0.724
2009 Yang S, Makowski L, Roux B. X-ray Solution Scattering Combined with Computation Characterizing Protein Folds and Multiple Conformational States: Computation and Application Biophysical Journal. 96: 411a. DOI: 10.1016/J.Bpj.2008.12.2096  0.685
2009 Sandtner W, Egwolf B, Roux B, Correa AM, Bezanilla F. Optical force measurements utilizing Lanthanide Binding Tags Biophysical Journal. 96: 402a-403a. DOI: 10.1016/J.Bpj.2008.12.2048  0.384
2009 Li Y, Allen TW, Andersen OS, Roux B. Potential of Mean Force Calculations of Ion Permeation in Gramicidin A Channel Biophysical Journal. 96: 365a. DOI: 10.1016/J.Bpj.2008.12.1966  0.628
2008 Truchon JF, Nicholls A, Iftimie RI, Roux B, Bayly CI. Accurate Molecular Polarizabilities Based on Continuum Electrostatics. Journal of Chemical Theory and Computation. 4: 1480-1493. PMID 23646034 DOI: 10.1021/Ct800123C  0.32
2008 Park S, Lau AY, Roux B. Computing conformational free energy by deactivated morphing. The Journal of Chemical Physics. 129: 134102. PMID 19045073 DOI: 10.1063/1.2982170  0.554
2008 Robertson JL, Palmer LG, Roux B. Long-pore electrostatics in inward-rectifier potassium channels. The Journal of General Physiology. 132: 613-32. PMID 19001143 DOI: 10.1085/Jgp.200810068  0.738
2008 Sompornpisut P, Roux B, Perozo E. Structural refinement of membrane proteins by restrained molecular dynamics and solvent accessibility data. Biophysical Journal. 95: 5349-61. PMID 18676641 DOI: 10.1529/Biophysj.108.142984  0.635
2008 Roux B. The membrane potential and its representation by a constant electric field in computer simulations. Biophysical Journal. 95: 4205-16. PMID 18641071 DOI: 10.1529/Biophysj.108.136499  0.426
2008 Roux B, Andersen OS, Allen TW. Comment on "Free energy simulations of single and double ion occupancy in gramicidin A" [J. Chem. Phys. 126, 105103 (2007)]. The Journal of Chemical Physics. 128: 227101; author reply. PMID 18554067 DOI: 10.1063/1.2931568  0.608
2008 Jo S, Vargyas M, Vasko-Szedlar J, Roux B, Im W. PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Research. 36: W270-5. PMID 18508808 DOI: 10.1093/Nar/Gkn314  0.664
2008 Lewis A, Jogini V, Blachowicz L, Lainé M, Roux B. Atomic constraints between the voltage sensor and the pore domain in a voltage-gated K+ channel of known structure. The Journal of General Physiology. 131: 549-61. PMID 18504314 DOI: 10.1085/Jgp.200809962  0.407
2008 Sezer D, Freed JH, Roux B. Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix. The Journal of Physical Chemistry. B. 112: 5755-67. PMID 18412413 DOI: 10.1021/Jp711375X  0.306
2008 Yang S, Roux B. Src kinase conformational activation: thermodynamics, pathways, and mechanisms. Plos Computational Biology. 4: e1000047. PMID 18369437 DOI: 10.1371/Journal.Pcbi.1000047  0.695
2008 Deng Y, Roux B. Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations. The Journal of Chemical Physics. 128: 115103. PMID 18361618 DOI: 10.1063/1.2842080  0.394
2008 Vásquez V, Sotomayor M, Cortes DM, Roux B, Schulten K, Perozo E. Three-dimensional architecture of membrane-embedded MscS in the closed conformation. Journal of Molecular Biology. 378: 55-70. PMID 18343404 DOI: 10.1016/J.Jmb.2007.10.086  0.691
2008 Harder E, Anisimov VM, Whitfield T, MacKerell AD, Roux B. Understanding the dielectric properties of liquid amides from a polarizable force field Journal of Physical Chemistry B. 112: 3509-3521. PMID 18302362 DOI: 10.1021/Jp709729D  0.319
2008 Pan AC, Sezer D, Roux B. Finding transition pathways using the string method with swarms of trajectories. The Journal of Physical Chemistry. B. 112: 3432-40. PMID 18290641 DOI: 10.1021/Jp0777059  0.307
2008 Noskov SY, Roux B. Control of ion selectivity in LeuT: two Na+ binding sites with two different mechanisms. Journal of Molecular Biology. 377: 804-18. PMID 18280500 DOI: 10.1016/J.Jmb.2008.01.015  0.611
2008 Banavali NK, Roux B. The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation. Structure (London, England : 1993). 13: 1715-23. PMID 16271895 DOI: 10.1016/J.Str.2005.09.005  0.302
2008 Deng Y, Roux B. Publisher’s Note: “Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations” [J. Chem. Phys. 128, 115103 (2008)] The Journal of Chemical Physics. 129: 139901. DOI: 10.1063/1.2936211  0.373
2008 Roux B. Chapter 13 A Brief Introduction to Voltage-Gated K+ Channels Current Topics in Membranes. 60: 369-384. DOI: 10.1016/S1063-5823(08)00013-6  0.406
2007 Whitfield TW, Varma S, Harder E, Lamoureux G, Rempe SB, Roux B. A theoretical study of aqueous solvation of K comparing ab initio, polarizable, and fixed-charge models. Journal of Chemical Theory and Computation. 3: 2068-2082. PMID 21785577 DOI: 10.1021/Ct700172B  0.625
2007 Anisimov VM, Vorobyov IV, Roux B, Mackerell AD. Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. Journal of Chemical Theory and Computation. 3: 1927-1946. PMID 18802495 DOI: 10.1021/Ct700100A  0.323
2007 Lau AY, Roux B. The free energy landscapes governing conformational changes in a glutamate receptor ligand-binding domain. Structure (London, England : 1993). 15: 1203-14. PMID 17937910 DOI: 10.1016/J.Str.2007.07.015  0.591
2007 Cordero-Morales JF, Jogini V, Lewis A, Vásquez V, Cortes DM, Roux B, Perozo E. Molecular driving forces determining potassium channel slow inactivation. Nature Structural & Molecular Biology. 14: 1062-9. PMID 17922012 DOI: 10.1038/Nsmb1309  0.622
2007 Pathak MM, Yarov-Yarovoy V, Agarwal G, Roux B, Barth P, Kohout S, Tombola F, Isacoff EY. Closing in on the resting state of the Shaker K(+) channel. Neuron. 56: 124-40. PMID 17920020 DOI: 10.1016/J.Neuron.2007.09.023  0.436
2007 Roux B. A proton-controlled check valve for sodium ion transport. Nature Chemical Biology. 3: 609-10. PMID 17876316 DOI: 10.1038/Nchembio1007-609  0.346
2007 Jogini V, Roux B. Dynamics of the Kv1.2 voltage-gated K+ channel in a membrane environment. Biophysical Journal. 93: 3070-82. PMID 17704179 DOI: 10.1529/Biophysj.107.112540  0.415
2007 Faraldo-Gómez JD, Roux B. On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases. Proceedings of the National Academy of Sciences of the United States of America. 104: 13643-8. PMID 17699616 DOI: 10.1073/Pnas.0704041104  0.34
2007 Campos FV, Chanda B, Roux B, Bezanilla F. Two atomic constraints unambiguously position the S4 segment relative to S1 and S2 segments in the closed state of Shaker K channel. Proceedings of the National Academy of Sciences of the United States of America. 104: 7904-9. PMID 17470814 DOI: 10.1073/Pnas.0702638104  0.358
2007 Lopes PE, Lamoureux G, Roux B, Mackerell AD. Polarizable empirical force field for aromatic compounds based on the classical drude oscillator. The Journal of Physical Chemistry. B. 111: 2873-85. PMID 17388420 DOI: 10.1021/Jp0663614  0.558
2007 Banavali NK, Roux B. Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck. Proteins. 67: 1096-112. PMID 17380483 DOI: 10.1002/Prot.21334  0.33
2007 Faraldo-Gómez JD, Roux B. Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: assessing entropic and environmental effects. Journal of Computational Chemistry. 28: 1634-47. PMID 17342721 DOI: 10.1002/Jcc.20652  0.438
2007 Noskov SY, Roux B. Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels. The Journal of General Physiology. 129: 135-43. PMID 17227917 DOI: 10.1085/Jgp.200609633  0.636
2007 Roux B. Extracellular blockade of potassium channels by TEA+: the tip of the iceberg? The Journal of General Physiology. 128: 635-6. PMID 17130517 DOI: 10.1085/Jgp.200609684  0.342
2007 Roux B. Dissecting the coupling between the voltage sensor and pore domains. Neuron. 52: 568-9. PMID 17114039 DOI: 10.1016/J.Neuron.2006.11.002  0.341
2007 Faraldo-Gómez JD, Kutluay E, Jogini V, Zhao Y, Heginbotham L, Roux B. Mechanism of intracellular block of the KcsA K+ channel by tetrabutylammonium: insights from X-ray crystallography, electrophysiology and replica-exchange molecular dynamics simulations. Journal of Molecular Biology. 365: 649-62. PMID 17070844 DOI: 10.1016/J.Jmb.2006.09.069  0.486
2007 Roux B, Simonson T. Implicit solvent models. Biophysical Chemistry. 78: 1-20. PMID 17030302 DOI: 10.1016/S0301-4622(98)00226-9  0.331
2007 Jogini V, Roux B. Corrigendum to "Electrostatics of the Intracellular Vestibule of K+ Channels" [J. Mol. Biol. 354 (2006) 272-288] (DOI:10.1016/j.jmb.2005.09.031) Journal of Molecular Biology. 373: 1374. DOI: 10.1016/J.Jmb.2005.09.102  0.329
2006 Harder E, Anisimov VM, Vorobyov IV, Lopes PE, Noskov SY, MacKerell AD, Roux B. Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. 2: 1587-97. PMID 26627029 DOI: 10.1021/Ct600180X  0.587
2006 Deng Y, Roux B. Calculation of Standard Binding Free Energies:  Aromatic Molecules in the T4 Lysozyme L99A Mutant. Journal of Chemical Theory and Computation. 2: 1255-73. PMID 26626834 DOI: 10.1021/Ct060037V  0.367
2006 Murcia M, Faráldo-Gómez JD, Maxfield FR, Roux B. Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol. Journal of Lipid Research. 47: 2614-30. PMID 16990645 DOI: 10.1194/Jlr.M600232-Jlr200  0.371
2006 Wang J, Deng Y, Roux B. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophysical Journal. 91: 2798-814. PMID 16844742 DOI: 10.1529/Biophysj.106.084301  0.415
2006 Noskov SY, Roux B. Ion selectivity in potassium channels. Biophysical Chemistry. 124: 279-91. PMID 16843584 DOI: 10.1016/J.Bpc.2006.05.033  0.642
2006 Allen TW, Andersen OS, Roux B. Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels. Biophysical Chemistry. 124: 251-67. PMID 16781050 DOI: 10.1016/J.Bpc.2006.04.015  0.629
2006 Cordero-Morales JF, Cuello LG, Zhao Y, Jogini V, Cortes DM, Roux B, Perozo E. Molecular determinants of gating at the potassium-channel selectivity filter. Nature Structural & Molecular Biology. 13: 311-8. PMID 16532009 DOI: 10.1038/Nsmb1069  0.614
2006 Allen TW, Andersen OS, Roux B. Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields. Biophysical Journal. 90: 3447-68. PMID 16500984 DOI: 10.1529/Biophysj.105.077073  0.628
2006 Lamoureux G, Roux B. Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field. The Journal of Physical Chemistry. B. 110: 3308-22. PMID 16494345 DOI: 10.1021/Jp056043P  0.61
2006 Zhao Y, Jogini V, Perozo E, Roux B. S3h1-1 Molecular Determinants of Gating at the K^+ Channel Selectivity Filter, Probed by Protein Crystallography and Molecular Dynamics Simulations(S3-h1: "Structural Aspects of Channel and Transporter Proteins",Symposia,Abstract,Meeting Program of EABS & BSJ 2006) Seibutsu Butsuri. 46: S139. DOI: 10.2142/Biophys.46.S139_3  0.636
2006 Harder E, Anisimov VM, Vorobyov IV, Lopes PEM, Noskov SY, MacKerell AD, Roux B. Atomic level anisotropy in the electrostatic modeling of lone pairs for a polarizable force field based on the classical drude oscillator Journal of Chemical Theory and Computation. 2: 1587-1597. DOI: 10.1021/ct600180x  0.484
2006 Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD. A polarizable model of water for molecular dynamics simulations of biomolecules Chemical Physics Letters. 418: 245-249. DOI: 10.1016/J.Cplett.2005.10.135  0.58
2005 Anisimov VM, Lamoureux G, Vorobyov IV, Huang N, Roux B, MacKerell AD. Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. 1: 153-68. PMID 26641126 DOI: 10.1021/Ct049930P  0.586
2005 Noskov SY, Lamoureux G, Roux B. Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field. The Journal of Physical Chemistry. B. 109: 6705-13. PMID 16851754 DOI: 10.1021/Jp045438Q  0.672
2005 Lagüe P, Roux B, Pastor RW. Molecular dynamics simulations of the influenza hemagglutinin fusion peptide in micelles and bilayers: conformational analysis of peptide and lipids. Journal of Molecular Biology. 354: 1129-41. PMID 16297931 DOI: 10.1016/J.Jmb.2005.10.038  0.658
2005 Jogini V, Roux B. Electrostatics of the intracellular vestibule of K+ channels. Journal of Molecular Biology. 354: 272-88. PMID 16242718 DOI: 10.1016/J.Jmb.2005.09.031  0.426
2005 Robertson JL, Roux B. One channel: open and closed. Structure (London, England : 1993). 13: 1398-400. PMID 16216569 DOI: 10.1016/J.Str.2005.09.004  0.561
2005 Roux B. The art of dissecting the function of a potassium channel. Neuron. 47: 777-8. PMID 16157271 DOI: 10.1016/J.Neuron.2005.08.031  0.373
2005 Chanda B, Asamoah OK, Blunck R, Roux B, Bezanilla F. Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement. Nature. 436: 852-6. PMID 16094369 DOI: 10.1038/Nature03888  0.395
2005 Gilquin B, Braud S, Eriksson MA, Roux B, Bailey TD, Priest BT, Garcia ML, Ménez A, Gasparini S. A variable residue in the pore of Kv1 channels is critical for the high affinity of blockers from sea anemones and scorpions. The Journal of Biological Chemistry. 280: 27093-102. PMID 15890656 DOI: 10.1074/Jbc.M413626200  0.388
2005 Roux B. Ion conduction and selectivity in K(+) channels. Annual Review of Biophysics and Biomolecular Structure. 34: 153-71. PMID 15869387 DOI: 10.1146/Annurev.Biophys.34.040204.144655  0.431
2005 Banavali NK, Roux B. Free energy landscape of A-DNA to B-DNA conversion in aqueous solution. Journal of the American Chemical Society. 127: 6866-76. PMID 15869310 DOI: 10.1021/Ja050482K  0.335
2005 Woo HJ, Roux B. Calculation of absolute protein-ligand binding free energy from computer simulations. Proceedings of the National Academy of Sciences of the United States of America. 102: 6825-30. PMID 15867154 DOI: 10.1073/Pnas.0409005102  0.377
2005 Bernèche S, Roux B. A gate in the selectivity filter of potassium channels. Structure (London, England : 1993). 13: 591-600. PMID 15837197 DOI: 10.1016/J.Str.2004.12.019  0.4
2005 Kutluay E, Roux B, Heginbotham L. Rapid intracellular TEA block of the KcsA potassium channel. Biophysical Journal. 88: 1018-29. PMID 15556975 DOI: 10.1529/Biophysj.104.052043  0.382
2005 Roux B, Schulten K. Computational studies of membrane channels. Structure (London, England : 1993). 12: 1343-51. PMID 15296727 DOI: 10.1016/J.Str.2004.06.013  0.553
2005 Anisimov VM, Lamoureux G, Vorobyov IV, Huang N, Roux B, MacKerell AD. Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator Journal of Chemical Theory and Computation. 1: 153-168. DOI: 10.1021/ct049930p  0.47
2004 Roux B, Allen T, Bernèche S, Im W. Theoretical and computational models of biological ion channels. Quarterly Reviews of Biophysics. 37: 15-103. PMID 17390604 DOI: 10.1017/S0033583504003968  0.704
2004 Allen TW, Andersen OS, Roux B. On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation. The Journal of General Physiology. 124: 679-90. PMID 15572347 DOI: 10.1085/Jgp.200409111  0.621
2004 Noskov SY, Bernèche S, Roux B. Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature. 431: 830-4. PMID 15483608 DOI: 10.1038/Nature02943  0.638
2004 Noskov SY, Im W, Roux B. Ion permeation through the alpha-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory. Biophysical Journal. 87: 2299-309. PMID 15454431 DOI: 10.1529/Biophysj.104.044008  0.711
2004 Chakrabarti N, Roux B, Pomès R. Structural determinants of proton blockage in aquaporins. Journal of Molecular Biology. 343: 493-510. PMID 15451676 DOI: 10.1016/J.Jmb.2004.08.036  0.655
2004 Woo HJ, Dinner AR, Roux B. Grand canonical Monte Carlo simulations of water in protein environments. The Journal of Chemical Physics. 121: 6392-400. PMID 15446937 DOI: 10.1063/1.1784436  0.613
2004 Faraldo-Gómez JD, Roux B. Electrostatics of ion stabilization in a ClC chloride channel homologue from Escherichia coli. Journal of Molecular Biology. 339: 981-1000. PMID 15165864 DOI: 10.1016/J.Jmb.2004.04.023  0.409
2004 Lainé M, Papazian DM, Roux B. Critical assessment of a proposed model of Shaker. Febs Letters. 564: 257-63. PMID 15111106 DOI: 10.1016/S0014-5793(04)00273-X  0.403
2004 Chakrabarti N, Tajkhorshid E, Roux B, Pomès R. Molecular basis of proton blockage in aquaporins. Structure (London, England : 1993). 12: 65-74. PMID 14725766 DOI: 10.1016/J.Str.2003.11.017  0.625
2004 Allen TW, Andersen OS, Roux B. Energetics of ion conduction through the gramicidin channel. Proceedings of the National Academy of Sciences of the United States of America. 101: 117-22. PMID 14691245 DOI: 10.1073/Pnas.2635314100  0.635
2004 Deng Y, Roux B. Hydration of Amino Acid Side Chains:  Nonpolar and Electrostatic Contributions Calculated from Staged Molecular Dynamics Free Energy Simulations with Explicit Water Molecules The Journal of Physical Chemistry B. 108: 16567-16576. DOI: 10.1021/Jp048502C  0.391
2003 Allen TW, Andersen OS, Roux B. Structure of gramicidin a in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data. Journal of the American Chemical Society. 125: 9868-77. PMID 12904055 DOI: 10.1021/Ja029317K  0.6
2003 Lainé M, Lin MC, Bannister JP, Silverman WR, Mock AF, Roux B, Papazian DM. Atomic proximity between S4 segment and pore domain in Shaker potassium channels. Neuron. 39: 467-81. PMID 12895421 DOI: 10.1016/S0896-6273(03)00468-9  0.402
2003 Bernèche S, Roux B. A microscopic view of ion conduction through the K+ channel. Proceedings of the National Academy of Sciences of the United States of America. 100: 8644-8. PMID 12837936 DOI: 10.1073/Pnas.1431750100  0.459
2003 Silverman WR, Roux B, Papazian DM. Structural basis of two-stage voltage-dependent activation in K+ channels. Proceedings of the National Academy of Sciences of the United States of America. 100: 2935-40. PMID 12606713 DOI: 10.1073/Pnas.0636603100  0.388
2003 Eriksson MA, Roux B. 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. Biophysical Journal. 83: 2595-609. PMID 12414693 DOI: 10.1016/S0006-3495(02)75270-3  0.436
2003 Roux B. Computational studies of the gramicidin channel. Accounts of Chemical Research. 35: 366-75. PMID 12069621 DOI: 10.1021/Ar010028V  0.47
2003 Lamoureux G, MacKerell AD, Roux B. A simple polarizable model of water based on classical drude oscillators Journal of Chemical Physics. 119: 5185-5197. DOI: 10.1063/1.1598191  0.573
2003 Lamoureux G, Roux B. Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm Journal of Chemical Physics. 119: 3025-3039. DOI: 10.1063/1.1589749  0.591
2002 Im W, Roux B. Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory. Journal of Molecular Biology. 322: 851-69. PMID 12270719 DOI: 10.1016/S0022-2836(02)00778-7  0.595
2002 Yang L, Beard W, Wilson S, Roux B, Broyde S, Schlick T. Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus. Journal of Molecular Biology. 321: 459-78. PMID 12162959 DOI: 10.1016/S0022-2836(02)00617-4  0.311
2002 Simoes M, Garneau L, Klein H, Banderali U, Hobeila F, Roux B, Parent L, Sauvé R. Cysteine mutagenesis and computer modeling of the S6 region of an intermediate conductance IKCa channel. The Journal of General Physiology. 120: 99-116. PMID 12084779 DOI: 10.1085/Jgp.20028586  0.655
2002 Im W, Roux B. 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. Journal of Molecular Biology. 319: 1177-97. PMID 12079356 DOI: 10.1016/S0022-2836(02)00380-7  0.614
2002 Pomès R, Roux B. Molecular mechanism of H+ conduction in the single-file water chain of the gramicidin channel. Biophysical Journal. 82: 2304-16. PMID 11964221 DOI: 10.1016/S0006-3495(02)75576-8  0.614
2002 Roux B. Theoretical and computational models of ion channels. Current Opinion in Structural Biology. 12: 182-9. PMID 11959495 DOI: 10.1016/S0959-440X(02)00307-X  0.393
2002 Roux B, Bernèche S. On the potential functions used in molecular dynamics simulations of ion channels. Biophysical Journal. 82: 1681-4. PMID 11898796 DOI: 10.1016/S0006-3495(02)75520-3  0.397
2002 Philippsen A, Im W, Engel A, Schirmer T, Roux B, Müller DJ. Imaging the electrostatic potential of transmembrane channels: atomic probe microscopy of OmpF porin. Biophysical Journal. 82: 1667-76. PMID 11867478 DOI: 10.1016/S0006-3495(02)75517-3  0.532
2002 Bernèche S, Roux B. The ionization state and the conformation of Glu-71 in the KcsA K(+) channel. Biophysical Journal. 82: 772-80. PMID 11806919 DOI: 10.1016/S0006-3495(02)75439-8  0.433
2002 Banavali NK, Im W, Roux B. Electrostatic free energy calculations using the generalized solvent boundary potential method The Journal of Chemical Physics. 117: 7381-7388. DOI: 10.1063/1.1507108  0.557
2002 Parent L, Sauvé R, Bernèche S, Roux B. A bas les barrières… d’énergie dans les canaux potassiques ! M S-Medecine Sciences. 18: 605-609. DOI: 10.1051/Medsci/2002185605  0.608
2002 Banavali NK, Roux B. Atomic Radii for Continuum Electrostatics Calculations on Nucleic Acids The Journal of Physical Chemistry B. 106: 11026-11035. DOI: 10.1021/Jp025852V  0.366
2002 Roux B. What can be deduced about the structure of Shaker from available data Novartis Foundation Symposium. 245: 84-108. DOI: 10.1002/0470868759.Ch7  0.416
2001 Bernèche S, Roux B. Energetics of ion conduction through the K+ channel. Nature. 414: 73-7. PMID 11689945 DOI: 10.1038/35102067  0.405
2001 Crouzy S, Bernèche S, Roux B. Extracellular blockade of K(+) channels by TEA: results from molecular dynamics simulations of the KcsA channel. The Journal of General Physiology. 118: 207-18. PMID 11479347 DOI: 10.1085/Jgp.118.2.207  0.445
2001 Lagüe P, Zuckermann MJ, Roux B. Lipid-mediated interactions between intrinsic membrane proteins: dependence on protein size and lipid composition. Biophysical Journal. 81: 276-84. PMID 11423413 DOI: 10.1016/S0006-3495(01)75698-6  0.674
2001 Young MA, Gonfloni S, Superti-Furga G, Roux B, Kuriyan J. Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell. 105: 115-26. PMID 11301007 DOI: 10.1016/S0092-8674(01)00301-4  0.521
2001 Schumaker MF, Pomès R, Roux B. Framework model for single proton conduction through gramicidin. Biophysical Journal. 80: 12-30. PMID 11159380 DOI: 10.1016/S0006-3495(01)75992-9  0.594
2001 Nina M, Bernèche S, Roux B. Anchoring of a monotopic membrane protein: the binding of prostaglandin H2 synthase-1 to the surface of a phospholipid bilayer. European Biophysics Journal : Ebj. 29: 439-54. PMID 11081405 DOI: 10.1007/Pl00006649  0.383
2001 Im W, Roux B. Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry The Journal of Chemical Physics. 115: 4850-4861. DOI: 10.1063/1.1390507  0.587
2001 Im W, Bernèche S, Roux B. Generalized solvent boundary potential for computer simulations The Journal of Chemical Physics. 114: 2924-2937. DOI: 10.1063/1.1336570  0.512
2001 Souaille M, Roux B. Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations Computer Physics Communications. 135: 40-57. DOI: 10.1016/S0010-4655(00)00215-0  0.363
2000 Lagüe P, Zuckermann MJ, Roux B. Lipid-mediated interactions between intrinsic membrane proteins: a theoretical study based on integral equations. Biophysical Journal. 79: 2867-79. PMID 11106595 DOI: 10.1016/S0006-3495(00)76524-6  0.675
2000 Schumaker MF, Pomès R, Roux B. A combined molecular dynamics and diffusion model of single proton conduction through gramicidin. Biophysical Journal. 79: 2840-57. PMID 11106593 DOI: 10.1016/S0006-3495(00)76522-2  0.625
2000 Roux B, Bernèche S, Im W. Ion channels, permeation, and electrostatics: insight into the function of KcsA. Biochemistry. 39: 13295-306. PMID 11063565 DOI: 10.1021/Bi001567V  0.547
2000 Im W, Seefeld S, Roux B. A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. Biophysical Journal. 79: 788-801. PMID 10920012 DOI: 10.1016/S0006-3495(00)76336-3  0.581
2000 Bernèche S, Roux B. Molecular Dynamics of the KcsA K+ Channel in a Bilayer Membrane Biophysical Journal. 78: 2900-2917. PMID 10827971 DOI: 10.1016/S0006-3495(00)76831-7  0.434
2000 Shobana S, Roux B, Andersen OS. Free Energy Simulations: Thermodynamic Reversibility and Variability Journal of Physical Chemistry B. 104: 5179-5190. DOI: 10.1021/Jp994193S  0.325
1999 Nina M, Im W, Roux B. Optimized atomic radii for protein continuum electrostatics solvation forces. Biophysical Chemistry. 78: 89-96. PMID 17030305 DOI: 10.1016/S0301-4622(98)00236-1  0.539
1999 Roux B, Woolf TB. The binding site of sodium in the gramicidin A channel. Novartis Foundation Symposium. 225: 113-24; discussion 1. PMID 10472051 DOI: 10.1002/9780470515716.Ch8  0.735
1999 Roux B, MacKinnon R. The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations. Science (New York, N.Y.). 285: 100-2. PMID 10390357 DOI: 10.1126/Science.285.5424.100  0.425
1999 Roux B. Statistical mechanical equilibrium theory of selective ion channels. Biophysical Journal. 77: 139-53. PMID 10388746 DOI: 10.1016/S0006-3495(99)76878-5  0.448
1999 Baudry J, Crouzy S, Roux B, Smith JC. Simulation analysis of the retinal conformational equilibrium in dark-adapted bacteriorhodopsin. Biophysical Journal. 76: 1909-17. PMID 10096888 DOI: 10.1016/S0006-3495(99)77349-2  0.745
1999 Pomès R, Eisenmesser E, Post CB, Roux B. Calculating excess chemical potentials using dynamic simulations in the fourth dimension The Journal of Chemical Physics. 111: 3387-3395. DOI: 10.1063/1.479622  0.622
1999 Crouzy S, Baudry J, Smith JC, Roux B. 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 Journal of Computational Chemistry. 20: 1644-1658. DOI: 10.1002/(Sici)1096-987X(19991130)20:15<1644::Aid-Jcc5>3.0.Co;2-Y  0.696
1998 MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FT, Mattos C, ... ... Roux B, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry. B. 102: 3586-616. PMID 24889800 DOI: 10.1021/Jp973084F  0.789
1998 Lagüe P, Zuckermann MJ, Roux B. Protein inclusion in lipid membranes: a theory based on the hypernetted chain integral equation. Faraday Discussions. 165-72; discussion 2. PMID 10822607 DOI: 10.1039/A807109H  0.663
1998 Marchand S, Roux B. Molecular dynamics study of calbindin D9k in the apo and singly and doubly calcium-loaded states. Proteins. 33: 265-84. PMID 9779793 DOI: 10.1002/(Sici)1097-0134(19981101)33:2<265::Aid-Prot10>3.0.Co;2-I  0.374
1998 Bernèche S, Nina M, Roux B. Molecular Dynamics Simulation of Melittin in a Dimyristoylphosphatidylcholine Bilayer Membrane Biophysical Journal. 75: 1603-1618. PMID 9746504 DOI: 10.1016/S0006-3495(98)77604-0  0.382
1998 Pomès R, Roux B. Free energy profiles for H+ conduction along hydrogen-bonded chains of water molecules. Biophysical Journal. 75: 33-40. PMID 9649365 DOI: 10.1016/S0006-3495(98)77492-2  0.604
1998 Roux B. Molecular dynamics simulations of ion channels: how far have we gone and where are we heading? Biophysical Journal. 74: 2744-5. PMID 9635728 DOI: 10.1016/S0006-3495(98)77981-0  0.455
1998 Roux B. Influence of the membrane potential on the free energy of an intrinsic protein. Biophysical Journal. 73: 2980-9. PMID 9414213 DOI: 10.1016/S0006-3495(97)78327-9  0.369
1998 Im W, Beglov D, Roux B. Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation Computer Physics Communications. 111: 59-75. DOI: 10.1016/S0010-4655(98)00016-2  0.517
1998 Chakrabarti N, Carrington Jr T, Roux B. Rate constants in quantum mechanical systems: A rigorous and practical path-integral formulation for computer simulations Chemical Physics Letters. 293: 209-220. DOI: 10.1016/S0009-2614(98)00736-2  0.319
1997 Ketchem RR, Roux B, Cross TA. High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints Structure. 5: 1655-1669. PMID 9438865 DOI: 10.1016/S0969-2126(97)00312-2  0.324
1997 Belohorcová K, Davis JH, Woolf TB, Roux B. Structure and dynamics of an amphiphilic peptide in a lipid bilayer: a molecular dynamics study. Biophysical Journal. 73: 3039-55. PMID 9414218 DOI: 10.1016/S0006-3495(97)78332-2  0.688
1997 Mohanty D, Elber R, Thirumalai D, Beglov D, Roux B. Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. Journal of Molecular Biology. 272: 423-42. PMID 9325101 DOI: 10.1006/Jmbi.1997.1246  0.584
1997 Woolf TB, Roux B. The binding site of sodium in the gramicidin A channel: comparison of molecular dynamics with solid-state NMR data. Biophysical Journal. 72: 1930-45. PMID 9129798 DOI: 10.1016/S0006-3495(97)78839-8  0.739
1997 Petrescu AJ, Receveur V, Calmettes P, Durand D, Desmadril M, Roux B, Smith JC. Small-angle neutron scattering by a strongly denatured protein: analysis using random polymer theory. Biophysical Journal. 72: 335-42. PMID 8994618 DOI: 10.1016/S0006-3495(97)78672-7  0.539
1997 Roux B. Valence selectivity of the gramicidin channel: a molecular dynamics free energy perturbation study. Biophysical Journal. 71: 3177-85. PMID 8968588 DOI: 10.1016/S0006-3495(96)79511-5  0.443
1997 Hinsen K, Roux B. Potential of mean force and reaction rates for proton transfer in acetylacetone The Journal of Chemical Physics. 106: 3567-3577. DOI: 10.1063/1.473439  0.346
1997 Beglov D, Roux B. An Integral Equation To Describe the Solvation of Polar Molecules in Liquid Water The Journal of Physical Chemistry B. 101: 7821-7826. DOI: 10.1021/Jp971083H  0.322
1997 Nina M, Beglov D, Roux B. Atomic Radii for Continuum Electrostatics Calculations Based on Molecular Dynamics Free Energy Simulations The Journal of Physical Chemistry B. 101: 5239-5248. DOI: 10.1021/Jp970736R  0.381
1997 and IG, Roux B. Interaction of K+ with a Phospholipid Bilayer: A Molecular Dynamics Study Journal of Physical Chemistry B. 101: 6066-6072. DOI: 10.1021/Jp9640134  0.429
1997 Baudry J, Crouzy S, Roux B, Smith JC. Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational Energetics Journal of Chemical Information and Computer Sciences. 37: 1018-1024. DOI: 10.1021/Ci9702398  0.742
1997 Sharafeddin OA, Hinsen K, Carrington T, Roux B. Mixing quantum-classical molecular dynamics methods applied to intramolecular proton transfer in acetylacetone Journal of Computational Chemistry. 18: 1760-1772. DOI: 10.1002/(Sici)1096-987X(19971115)18:14<1760::Aid-Jcc5>3.0.Co;2-I  0.315
1997 Hinsen K, Roux B. A potential function for computer simulation studies of proton transfer in acetylacetone Journal of Computational Chemistry. 18: 368-380. DOI: 10.1002/(Sici)1096-987X(199702)18:3<368::Aid-Jcc7>3.0.Co;2-S  0.367
1996 Roux B, Nina M, Pomès R, Smith JC. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophysical Journal. 71: 670-81. PMID 8842206 DOI: 10.1016/S0006-3495(96)79267-6  0.738
1996 Pomès R, Roux B. Structure and dynamics of a proton wire: a theoretical study of H+ translocation along the single-file water chain in the gramicidin A channel. Biophysical Journal. 71: 19-39. PMID 8804586 DOI: 10.1016/S0006-3495(96)79211-1  0.606
1996 Woolf TB, Roux B. Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer. Proteins. 24: 92-114. PMID 8628736 DOI: 10.1002/(Sici)1097-0134(199601)24:1<92::Aid-Prot7>3.0.Co;2-Q  0.724
1996 Pomès R, Roux B. Theoretical Study of H+Translocation along a Model Proton Wire The Journal of Physical Chemistry. 100: 2519-2527. DOI: 10.1021/Jp9525752  0.366
1995 Nina M, Roux B, Smith JC. Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water. Biophysical Journal. 68: 25-39. PMID 7711248 DOI: 10.1016/S0006-3495(95)80184-0  0.593
1995 Roux B, Prod'hom B, Karplus M. Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy. Biophysical Journal. 68: 876-92. PMID 7538804 DOI: 10.1016/S0006-3495(95)80264-X  0.66
1995 Roux B. The calculation of the potential of mean force using computer simulations Computer Physics Communications. 91: 275-282. DOI: 10.1016/0010-4655(95)00053-I  0.352
1995 Woolf TB, Malkin VG, Malkina OL, Salahub DR, Roux B. The backbone 15N chemical shift tensor of the gramicidin channel. A molecular dynamics and density functional study Chemical Physics Letters. 239: 186-194. DOI: 10.1016/0009-2614(95)00424-3  0.708
1995 Pomès R, Roux B. Quantum effects on the structure and energy of a protonated linear chain of hydrogen-bonded water molecules Chemical Physics Letters. 234: 416-424. DOI: 10.1016/0009-2614(95)00071-B  0.595
1995 Roux B, Karplus M. Potential energy function for cation-peptide interactions: Anab initio study Journal of Computational Chemistry. 16: 690-704. DOI: 10.1002/Jcc.540160605  0.606
1995 Beglov D, Roux B. Dominant solvation effects from the primary shell of hydration: Approximation for molecular dynamics simulations Biopolymers. 35: 171-178. DOI: 10.1002/Bip.360350205  0.412
1994 Crouzy S, Woolf TB, Roux B. A molecular dynamics study of gating in dioxolane-linked gramicidin A channels. Biophysical Journal. 67: 1370-86. PMID 7529578 DOI: 10.1016/S0006-3495(94)80618-6  0.726
1994 Woolf TB, Roux B. Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Proceedings of the National Academy of Sciences of the United States of America. 91: 11631-5. PMID 7526400 DOI: 10.1073/Pnas.91.24.11631  0.744
1994 Roux B, Karplus M. Molecular dynamics simulations of the gramicidin channel. Annual Review of Biophysics and Biomolecular Structure. 23: 731-61. PMID 7522667 DOI: 10.1146/Annurev.Bb.23.060194.003503  0.586
1994 Beglov D, Roux B. Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations The Journal of Chemical Physics. 100: 9050-9063. DOI: 10.1063/1.466711  0.327
1994 Woolf TB, Roux B. Conformational Flexibility of o-Phosphorylcholine and o-Phosphorylethanolamine: A Molecular Dynamics Study of Solvation Effects Journal of the American Chemical Society. 116: 5916-5926. DOI: 10.1021/Ja00092A048  0.659
1993 Calmettes P, Roux B, Durand D, Desmadril M, Smith JC. Configurational distribution of denatured phosphoglycerate kinase. Journal of Molecular Biology. 231: 840-8. PMID 8515454 DOI: 10.1006/Jmbi.1993.1330  0.591
1993 Thomas A, Roux B, Smith JC. Computer simulations of the flexibility of a series of synthetic cyclic peptide analogues. Biopolymers. 33: 1249-70. PMID 8364158 DOI: 10.1002/Bip.360330811  0.603
1993 Ferrand M, Zaccai G, Nina M, Smith JC, Etchebest C, Roux B. Structure and dynamics of bacteriorhodopsin. Comparison of simulation and experiment. Febs Letters. 327: 256-60. PMID 8348952 DOI: 10.1016/0014-5793(93)80999-B  0.614
1993 Roux B, Karplus M. Ion transport in the gramicidin channel: free energy of the solvated right-handed dimer in a model membrane Journal of the American Chemical Society. 115: 3250-3262. DOI: 10.1021/Ja00061A025  0.654
1993 Nina M, Smith J, Roux B. Ab initio quantum chemical analysis of Schiff base-water interactions in bacteriorhodopsin Journal of Molecular Structure: Theochem. 286: 231-245. DOI: 10.1016/0166-1280(93)87166-B  0.593
1993 Roux B. Non-additivity in cation—peptide interactions. A molecular dynamics and ab initio study of Na+ in the gramicidin channel Chemical Physics Letters. 212: 231-240. DOI: 10.1016/0009-2614(93)89319-D  0.447
1992 Brueschweiler R, Roux B, Blackledge M, Griesinger C, Karplus M, Ernst RR. Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution Journal of the American Chemical Society. 114: 2289-2302. DOI: 10.1021/Ja00033A002  0.57
1991 Roux B, Karplus M. Ion transport in a model gramicidin channel. Structure and thermodynamics. Biophysical Journal. 59: 961-81. PMID 1714305 DOI: 10.1016/S0006-3495(91)82311-6  0.648
1991 Roux B, Karplus M. Ion transport in a gramicidin-like channel: dynamics and mobility The Journal of Physical Chemistry. 95: 4856-4868. DOI: 10.1021/J100165A049  0.608
1990 Straub JE, Berne BJ, Roux B. Spatial dependence of time-dependent friction for pair diffusion in a simple fluid The Journal of Chemical Physics. 93: 6804-6812. DOI: 10.1063/1.458950  0.527
1990 Yu H, Roux B, Karplus M. Solvation thermodynamics: An approach from analytic temperature derivatives The Journal of Chemical Physics. 92: 5020-5033. DOI: 10.1063/1.458538  0.568
1990 Roux B, Yu HA, Karplus M. Molecular basis for the Born model of ion solvation The Journal of Physical Chemistry. 94: 4683-4688. DOI: 10.1021/J100374A057  0.59
1988 Roux B, Karplus M. The normal modes of the gramicidin-A dimer channel. Biophysical Journal. 53: 297-309. PMID 2450595 DOI: 10.1016/S0006-3495(88)83107-2  0.589
1985 Roux B, Sauvé R. A general solution to the time interval omission problem applied to single channel analysis. Biophysical Journal. 48: 149-158. PMID 2410047 DOI: 10.1016/S0006-3495(85)83768-1  0.623
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