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Benoit Roux, Ph.D. - Publications

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

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

Year Citation  Score
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  1
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  0.88
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  0.88
2019 Villa F, MacKerell AD, Roux B, Simonson T. Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg". The Journal of Physical Chemistry. A. PMID 30600990 DOI: 10.1021/acs.jpca.8b12337  1
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  0.88
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  0.84
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  0.68
2018 Pond MP, Blachowicz L, Roux B. H, N, and C resonance assignments of the intrinsically disordered SH4 and Unique domains of Hck. Biomolecular Nmr Assignments. PMID 30284668 DOI: 10.1007/s12104-018-9854-z  0.68
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  0.84
2018 Meng Y, Ahuja LG, Kornev AP, Taylor SS, Roux B. Corrigendum to "A Catalytically-Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation." J. Mol. Biol. 430(6) (Mar 16 2018), 881-889. Journal of Molecular Biology. PMID 30220583 DOI: 10.1016/j.jmb.2018.09.001  0.84
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  0.76
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  1
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  1
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  1
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  1
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  0.84
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  0.84
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  0.76
2018 Han K, Venable RM, Bryant AM, Legacy CJ, Shen R, Li H, Roux B, Gericke A, Pastor RW. Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions. The Journal of Physical Chemistry. B. PMID 29293344 DOI: 10.1021/acs.jpcb.7b10730  0.64
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  0.84
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  1
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  0.64
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  1
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  1
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  0.84
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  0.84
2017 Sadati M, Ramezani-Dakhel H, Bu W, Sevgen E, Liang Z, Erol C, Rahimi M, Taheri Qazvini N, Lin B, Abbott NL, Roux B, Schlossman ML, de Pablo JJ. Molecular Structure of Canonical Liquid Crystal Interfaces. Journal of the American Chemical Society. PMID 28177227 DOI: 10.1021/jacs.7b00167  0.68
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  0.44
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  0.88
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  1
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  0.76
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  0.84
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  0.88
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  1
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  0.88
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  0.88
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.68
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  0.32
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  1
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  1
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  1
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  1
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  0.88
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  1
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  1
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  1
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  0.6
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  1
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  1
2015 Chen Y, Roux B. Generalized Metropolis acceptance criterion for hybrid non-equilibrium molecular dynamics - Monte Carlo simulations Journal of Chemical Physics. 142. DOI: 10.1063/1.4904889  1
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  1
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  1
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  0.56
2014 Maragliano L, Roux B, Vanden-Eijnden E. Comparison between Mean Forces and Swarms-of-Trajectories String Methods. Journal of Chemical Theory and Computation. 10: 524-33. PMID 26580029 DOI: 10.1021/ct400606c  0.4
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  1
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  0.36
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  1
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  1
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  0.6
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  1
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  1
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  1
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  1
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  1
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: 10.1073/pnas.1320174111  1
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  1
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  0.84
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  1
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  1
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  1
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  1
2014 Weingarth M, van der Cruijsen EA, Ostmeyer J, Lievestro S, Roux B, Baldus M. Quantitative analysis of the water occupancy around the selectivity filter of a K+ channel in different gating modes. Journal of the American Chemical Society. 136: 2000-7. PMID 24410583 DOI: 10.1021/ja411450y  1
2014 Sezer D, Roux B. Markov state and diffusive stochastic models in electron spin resonance Advances in Experimental Medicine and Biology. 797: 115-138. PMID 24297280 DOI: 10.1007/978-94-007-7606-7-10  1
2014 Meng Y, Roux B. Locking the active conformation of c-Src kinase through the phosphorylation of the activation loop Journal of Molecular Biology. 426: 423-435. PMID 24103328 DOI: 10.1016/j.jmb.2013.10.001  1
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  1
2014 Kazmier K, Sharma S, Islam SM, Roux B, Mchaourab HS, Wright EM. 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: 14752-14757. DOI: 10.1073/pnas.1410431111/-/DCSupplemental  1
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  1
2014 Chen Y, Roux B. Efficient hybrid non-equilibrium molecular dynamics - Monte Carlo simulations with symmetric momentum reversal Journal of Chemical Physics. 141. DOI: 10.1063/1.4895516  1
2014 Andrew McCammon J, Roux B, Voth G, Yang W. Special issue on free energy Journal of Chemical Theory and Computation. 10: 2631. DOI: 10.1021/ct500366u  1
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: 2690-2709. DOI: 10.1021/ct500195p  1
2014 Maragliano L, Roux B, Vanden-Eijnden E. Comparison between mean forces and swarms-of-trajectories string methods Journal of Chemical Theory and Computation. 10: 524-533. DOI: 10.1021/ct400606c  1
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  1
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  0.6
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  1
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  1
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  0.64
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.84
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  1
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  1
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  1
2013 Roux B, Islam SM. Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy. The Journal of Physical Chemistry. B. 117: 4733-9. PMID 23510121 DOI: 10.1021/jp3110369  1
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  1
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  1
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  1
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  1
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: 10.1021/ja310777k  1
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  1
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  1
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  1
2013 Huang L, Roux B. Automated force field parameterization for nonpolarizable and polarizable atomic models based on ab initio target data Journal of Chemical Theory and Computation. 9: 3543-3556. DOI: 10.1021/ct4003477  1
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  1
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  1
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. DOI: 10.1021/ct300978b  1
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  0.84
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  0.96
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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. DOI: 10.1021/ct300468g  1
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  1
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  1
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  1
2011 Sandtner W, Egwolf B, Khalili-Araghi F, Sánchez-Rodríguez JE, Roux B, Bezanilla F, Holmgren M. Ouabain binding site in a functioning Na+/K+ ATPase. The Journal of Biological Chemistry. 286: 38177-83. PMID 21911500 DOI: 10.1074/jbc.M111.267682  1
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  1
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  1
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  1
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  1
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  1
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  1
2011 Lau AY, Roux B. Structural biology: One domain, multiple conformations. Nature Chemical Biology. 7: 130-1. PMID 21321548 DOI: 10.1038/nchembio.527  1
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: 10.1038/nsmb.2010  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2010 Roux B. Perspectives on: molecular dynamics and computational methods. The Journal of General Physiology. 135: 547-8. PMID 20513755 DOI: 10.1085/jgp.201010456  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.92
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: 10.1073/pnas.0811899106  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.48
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  1
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  1
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  1
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  1
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  0.48
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  0.76
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  1
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  1
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  1
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  1
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  0.48
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  1
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  1
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  1
2000 Roux B, Bernèche S, Im W. Ion channels, permeation, and electrostatics: insight into the function of KcsA. Biochemistry. 39: 13295-306. PMID 11063565  1
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  1
1999 Nina M, Im W, Roux B. Optimized atomic radii for protein continuum electrostatics solvation forces. Biophysical Chemistry. 78: 89-96. PMID 17030305  1
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  1
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  0.96
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  1
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  0.48
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  1
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  1
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  0.96
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  0.96
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  0.48
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  1
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  0.96
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  1
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  1
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  1
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  1
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  0.96
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  0.96
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  0.96
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  1
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  1
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