Year |
Citation |
Score |
2023 |
Blazhynska M, Gumbart JC, Chen H, Tajkhorshid E, Roux B, Chipot C. A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes. Journal of Chemical Theory and Computation. 19: 9077-9092. PMID 38091976 DOI: 10.1021/acs.jctc.3c00941 |
0.592 |
|
2023 |
Artigas P, Meyer DJ, Young VC, Spontarelli K, Eastman J, Strandquist E, Rui H, Roux B, Birk MA, Nakanishi H, Abe K, Gatto C. A Na pump with reduced stoichiometry is up-regulated by brine shrimp in extreme salinities. Proceedings of the National Academy of Sciences of the United States of America. 120: e2313999120. PMID 38079564 DOI: 10.1073/pnas.2313999120 |
0.455 |
|
2023 |
Shen R, Roux B, Perozo E. Anionic omega currents from single countercharge mutants in the voltage-sensing domain of Ci-VSP. The Journal of General Physiology. 156. PMID 38019193 DOI: 10.1085/jgp.202213311 |
0.529 |
|
2022 |
Shen R, Meng Y, Roux B, Perozo E. Mechanism of voltage gating in the voltage-sensing phosphatase Ci-VSP. Proceedings of the National Academy of Sciences of the United States of America. 119: e2206649119. PMID 36279472 DOI: 10.1073/pnas.2206649119 |
0.573 |
|
2022 |
Bignucolo O, Chipot C, Kellenberger S, Roux B. Galvani Offset Potential and Constant-pH Simulations of Membrane Proteins. The Journal of Physical Chemistry. B. 126: 6868-6877. PMID 36049129 DOI: 10.1021/acs.jpcb.2c04593 |
0.305 |
|
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 |
0.553 |
|
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 |
0.542 |
|
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 |
0.747 |
|
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 |
0.594 |
|
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 |
0.432 |
|
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 |
0.526 |
|
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 |
0.573 |
|
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 |
0.705 |
|
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 |
0.573 |
|
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 |
0.481 |
|
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 |
0.62 |
|
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 |
0.591 |
|
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 |
0.673 |
|
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 |
0.569 |
|
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 |
0.538 |
|
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 |
0.609 |
|
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 |
0.713 |
|
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 |
0.512 |
|
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 |
0.592 |
|
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 |
0.406 |
|
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 |
0.793 |
|
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 |
0.776 |
|
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 |
0.577 |
|
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 |
0.646 |
|
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 |
0.609 |
|
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 |
0.628 |
|
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 |
0.371 |
|
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 |
0.385 |
|
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 |
0.31 |
|
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 |
0.529 |
|
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 |
0.586 |
|
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 |
0.56 |
|
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 |
0.79 |
|
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 |
0.326 |
|
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 |
0.327 |
|
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 |
0.514 |
|
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 |
0.384 |
|
2017 |
Roux B. Ion channels and ion selectivity. Essays in Biochemistry. 61: 201-209. PMID 28487397 DOI: 10.1042/Ebc20160074 |
0.413 |
|
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 |
0.635 |
|
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 |
0.559 |
|
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 |
0.592 |
|
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 |
0.605 |
|
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 |
0.527 |
|
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 |
0.538 |
|
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 |
0.499 |
|
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 |
0.598 |
|
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 |
0.331 |
|
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 |
0.544 |
|
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 |
0.756 |
|
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 |
0.623 |
|
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 |
0.598 |
|
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 |
0.594 |
|
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 |
0.599 |
|
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 |
0.563 |
|
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 |
0.336 |
|
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 |
0.514 |
|
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 |
0.645 |
|
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 |
0.523 |
|
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 |
0.609 |
|
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 |
0.556 |
|
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 |
0.578 |
|
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 |
0.762 |
|
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 |
0.61 |
|
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 |
0.691 |
|
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 |
0.579 |
|
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 |
0.523 |
|
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 |
0.301 |
|
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 |
0.521 |
|
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 |
0.574 |
|
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 |
0.746 |
|
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 |
0.59 |
|
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 |
0.425 |
|
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 |
0.742 |
|
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 |
0.707 |
|
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 |
0.591 |
|
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 |
0.59 |
|
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 |
0.609 |
|
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 |
0.584 |
|
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 |
0.655 |
|
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 |
0.538 |
|
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 |
0.721 |
|
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 |
0.337 |
|
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 |
0.483 |
|
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 |
0.508 |
|
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 |
0.749 |
|
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 |
0.708 |
|
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 |
0.321 |
|
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 |
0.645 |
|
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 |
0.536 |
|
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 |
0.528 |
|
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 |
0.54 |
|
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 |
0.616 |
|
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 |
0.682 |
|
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 |
0.303 |
|
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 |
0.547 |
|
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 |
0.508 |
|
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 |
0.642 |
|
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 |
0.628 |
|
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 |
0.6 |
|
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 |
0.54 |
|
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 |
0.313 |
|
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 |
0.7 |
|
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 |
0.673 |
|
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 |
0.607 |
|
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 |
0.549 |
|
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 |
0.448 |
|
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 |
0.581 |
|
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 |
0.335 |
|
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 |
0.336 |
|
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 |
0.593 |
|
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 |
0.581 |
|
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 |
0.523 |
|
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 |
0.699 |
|
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 |
0.392 |
|
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 |
0.71 |
|
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 |
0.582 |
|
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 |
0.716 |
|
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 |
0.604 |
|
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 |
0.464 |
|
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 |
0.376 |
|
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 |
0.428 |
|
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 |
0.613 |
|
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 |
0.619 |
|
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 |
0.772 |
|
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 |
0.608 |
|
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 |
0.507 |
|
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 |
0.631 |
|
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 |
0.823 |
|
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 |
0.551 |
|
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 |
0.384 |
|
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 |
0.68 |
|
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 |
0.693 |
|
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 |
0.486 |
|
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 |
0.379 |
|
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 |
0.657 |
|
2011 |
Sandtner W, Egwolf B, Khalili-Araghi F, Sánchez-RodrÃguez 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 |
0.34 |
|
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 |
0.505 |
|
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 |
0.411 |
|
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 |
0.437 |
|
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 |
0.763 |
|
2011 |
Lau AY, Roux B. Structural biology: One domain, multiple conformations. Nature Chemical Biology. 7: 130-1. PMID 21321548 DOI: 10.1038/Nchembio.527 |
0.575 |
|
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 |
0.565 |
|
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 |
0.412 |
|
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 |
0.683 |
|
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 |
0.61 |
|
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 |
0.516 |
|
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 |
0.557 |
|
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 |
0.662 |
|
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 |
0.754 |
|
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 |
0.4 |
|
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 |
0.566 |
|
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 |
0.664 |
|
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 |
0.6 |
|
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 |
0.399 |
|
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 |
0.507 |
|
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 |
0.68 |
|
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 |
0.659 |
|
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 |
0.595 |
|
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 |
0.617 |
|
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 |
0.641 |
|
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 |
0.563 |
|
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 |
0.397 |
|
2010 |
Roux B. Perspectives on: molecular dynamics and computational methods. The Journal of General Physiology. 135: 547-8. PMID 20513755 DOI: 10.1083/Jcb1896Oia16 |
0.31 |
|
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 |
0.675 |
|
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 |
0.652 |
|
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 |
0.527 |
|
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 |
0.552 |
|
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 |
0.495 |
|
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 |
0.678 |
|
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 |
0.474 |
|
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 |
0.406 |
|
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 |
0.644 |
|
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 |
0.57 |
|
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 |
0.594 |
|
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 |
0.564 |
|
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 |
0.424 |
|
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 |
0.666 |
|
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 |
0.532 |
|
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 |
0.36 |
|
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 |
0.527 |
|
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 |
0.76 |
|
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 |
0.562 |
|
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 |
0.563 |
|
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 |
0.666 |
|
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 |
0.685 |
|
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 |
0.305 |
|
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 |
0.558 |
|
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 |
0.698 |
|
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 |
0.573 |
|
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 |
0.623 |
|
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 |
0.332 |
|
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 |
0.566 |
|
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 |
0.679 |
|
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 |
0.648 |
|
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 |
0.573 |
|
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 |
0.634 |
|
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 |
0.721 |
|
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 |
0.682 |
|
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 |
0.627 |
|
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 |
0.552 |
|
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 |
0.736 |
|
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 |
0.632 |
|
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 |
0.427 |
|
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 |
0.607 |
|
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 |
0.661 |
|
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 |
0.408 |
|
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 |
0.692 |
|
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 |
0.69 |
|
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 |
0.609 |
|
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 |
0.303 |
|
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 |
0.589 |
|
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 |
0.619 |
|
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 |
0.359 |
|
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 |
0.633 |
|
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 |
0.342 |
|
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 |
0.485 |
|
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 |
0.328 |
|
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 |
0.585 |
|
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 |
0.372 |
|
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 |
0.639 |
|
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 |
0.628 |
|
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 |
0.611 |
|
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 |
0.633 |
|
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 |
0.482 |
|
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 |
0.671 |
|
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 |
0.655 |
|
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 |
0.425 |
|
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 |
0.557 |
|
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 |
0.396 |
|
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 |
0.43 |
|
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 |
0.399 |
|
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 |
0.552 |
|
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 |
0.471 |
|
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 |
0.701 |
|
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 |
0.62 |
|
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 |
0.636 |
|
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 |
0.707 |
|
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 |
0.654 |
|
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 |
0.608 |
|
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 |
0.408 |
|
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 |
0.624 |
|
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 |
0.634 |
|
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 |
0.458 |
|
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 |
0.469 |
|
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 |
0.59 |
|
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 |
0.609 |
|
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 |
0.613 |
|
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 |
0.392 |
|
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 |
0.396 |
|
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 |
0.527 |
|
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 |
0.553 |
|
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 |
0.607 |
|
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 |
0.404 |
|
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 |
0.444 |
|
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 |
0.671 |
|
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 |
0.519 |
|
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 |
0.583 |
|
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 |
0.507 |
|
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 |
0.672 |
|
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 |
0.624 |
|
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 |
0.542 |
|
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 |
0.576 |
|
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 |
0.433 |
|
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 |
0.534 |
|
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 |
0.734 |
|
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 |
0.447 |
|
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 |
0.743 |
|
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 |
0.621 |
|
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 |
0.693 |
|
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 |
0.66 |
|
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 |
0.383 |
|
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 |
0.603 |
|
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 |
0.454 |
|
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 |
0.37 |
|
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 |
0.512 |
|
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 |
0.687 |
|
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 |
0.581 |
|
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 |
0.738 |
|
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 |
0.535 |
|
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 |
0.321 |
|
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 |
0.74 |
|
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 |
0.736 |
|
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 |
0.605 |
|
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 |
0.723 |
|
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 |
0.589 |
|
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 |
0.659 |
|
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 |
0.594 |
|
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 |
0.725 |
|
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 |
0.743 |
|
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 |
0.585 |
|
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 |
0.326 |
|
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 |
0.658 |
|
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 |
0.588 |
|
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 |
0.6 |
|
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 |
0.61 |
|
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 |
0.653 |
|
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 |
0.59 |
|
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 |
0.446 |
|
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 |
0.647 |
|
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 |
0.607 |
|
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 |
0.524 |
|
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 |
0.567 |
|
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 |
0.589 |
|
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 |
0.588 |
|
1985 |
Mithieux G, Chauvin F, Roux B, Rousset B. Association states of tubulin in the presence and absence of microtubule-associated proteins. Analysis by electric birefringence. Biophysical Chemistry. 22: 307-316. PMID 4063455 DOI: 10.1016/0301-4622(85)80054-5 |
0.3 |
|
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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