Publications



[ 2015 | 2014 | 2013 | 2012 | 2011 | 2008-2010 | 2006-2007 | 2004-2005 | 2000-2003 | 1997-1999 | 1985-1996 ]


2015


326. Shen, R., W. Han, G. Fiorin, S. M. Islam, K. Schulten, and B. Roux. 2015. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments. PLOS Comput. Biol. 11:e1004368.

325. Sanchez-Rodriguez, J. E., F. Khalili-Araghi, P. Miranda, B. Roux, M. Holmgren, and F. Bezanilla. 2015. A structural rearrangement of the Na+/K+-ATPase traps ouabain within the external ion permeation pathway. J Mol Biol 427:1335-1344.

324. Ngo, V., M. C. da Silva, M. Kubillus, H. Li, B. Roux, M. Elstner, Q. Cui, D. R. Salahub, and S. Y. Noskov. 2015. Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins. Journal of chemical theory and computation 11:4992-5001.

323. Meng, Y., and B. Roux. 2015. Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression. Journal of chemical theory and computation 11:3523-3529.

322. Meng, Y., and B. Roux. 2015. Computational study of the W260A activating mutant of Src tyrosine kinase. Protein Sci.

321. Meng, Y., Y. L. Lin, and B. Roux. 2015. Computational study of the "DFG-flip" conformational transition in c-Abl and c-Src tyrosine kinases. The journal of physical chemistry 119:1443-1456.

320. Martin, E., S. Knapp, R. A. Engh, H. Moebitz, T. Varin, B. Roux, J. Meiler, V. Berdini, A. Baumann, and M. Vieth. 2015. Perspective on computational and structural aspects of kinase discovery from IPK2014. Biochim Biophys Acta 1854:1595-1604.

319. Li, H., V. Ngo, M. C. Da Silva, D. R. Salahub, K. Callahan, B. Roux, and S. Y. Noskov. 2015. Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field. The journal of physical chemistry 119:9401-9416.

318. Lemkul, J. A., B. Roux, D. van der Spoel, and A. D. MacKerell, Jr. 2015. Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. J Comput Chem 36:1473-1479.

317. Jo, S., C. Chipot, and B. Roux. 2015. Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics. Journal of chemical theory and computation 11:2234-2244.

316. Islam, S. M., and B. Roux. 2015. Simulating the distance distribution between spin-labels attached to proteins. The journal of physical chemistry 119:3901-3911.

315. Islam, S. M., R. Cheng, A. R. Stein, H. Mchaourab, E. Tajkhorshid, L. R. Forrest, B. Roux, and M. C. Maduke. 2015. Monitoring H+-driven structural changes in a CLC chloride-proton antiporter using computationally-guided double electron-electron resonance spectroscopy.

314. Gaudet, R., B. Roux, and D. L. Minor, Jr. 2015. Insights into the molecular foundations of electrical excitation. J Mol Biol 427:1-2.

313. Dhakshnamoorthy, B., L. Blachowicz, H. Rui, and B. Roux. 2015. Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola.

312. Chen, Y., and B. Roux. 2015. Constant-pH Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulation Method. Journal of chemical theory and computation 11:3919-3931.

311. Chen, Y., and B. Roux. 2015. 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 11:3572-3583.

310. Chen, Y., and B. Roux. 2015. Generalized Metropolis acceptance criterion for hybrid non-equilibrium molecular dynamics-Monte Carlo simulations. The Journal of chemical physics 142:024101.

309. Castillo, J. P., H. Rui, D. Basilio, A. Das, B. Roux, R. Latorre, F. Bezanilla, and M. Holmgren. 2015. Mechanism of potassium ion uptake by the Na(+)/K(+)-ATPase. Nat Commun 6:7622.

Back to the top



2014


308. Weingarth, M., E. A. van der Cruijsen, J. Ostmeyer, S. Lievestro, B. Roux, and M. Baldus. 2014. Quantitative Analysis of the Water Occupancy around the Selectivity Filter of a K(+) Channel in Different Gating Modes. J. Am. Chem. Soc. 136:2000-2007.

307. Tietjen, G. T., Z. Gong, C. H. Chen, E. Vargas, J. E. Crooks, K. D. Cao, C. T. Heffern, J. M. Henderson, M. Meron, B. Lin, B. Roux, M. L. Schlossman, T. L. Steck, K. Y. Lee, and E. J. Adams. 2014. Molecular mechanism for differential recognition of membrane phosphatidylserine by the immune regulatory receptor Tim4. Proc. Natl. Acad. Sci. U.S.A. 111:E1463-1472.

306. Tempkin, J. O., B. Qi, M. G. Saunders, B. Roux, A. R. Dinner, and J. Weare. 2014. Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations. J. Chem. Phys. 140:184114.

305. Shukla, D., Y. Meng, B. Roux, and V. S. Pande. 2014. Activation pathway of Src kinase reveals intermediate states as targets for drug design. Nat Commun 5:3397.

304. Sezer, D., and B. Roux. 2014. Markov state and diffusive stochastic models in electron spin resonance. Adv Exp Med Biol 797:115-138.

303. Saunders, M. G., J. Tempkin, J. Weare, A. R. Dinner, B. Roux, and G. A. Voth. 2014. Nucleotide regulation of the structure and dynamics of G-actin. Biophysical journal 106:1710-1720.

302. Sánchez-Rodríguez, J. E., F. Khalili-Araghi, P. Miranda, B. Roux, M. Holmgren, and F. Bezanilla. 2014. Ouabain rearranges the external end of the ion permeation path of the Na+/K+-ATPase to become trapped. Structure.

301. Raghuraman, H., S. M. Islam, S. Mukherjee, B. Roux, and E. Perozo. 2014. Dynamics transitions at the outer vestibule of the KcsA potassium channel during gating. Proc Natl Acad Sci U S A 111:1831-1836.

300. Meng, Y., and B. Roux. 2014. Locking the Active Conformation of c-Src Kinase through the Phosphorylation of the Activation Loop. J. Mol. Biol. 426:423–435.

299. McCammon, J. A., B. Roux, G. Voth, and W. Yang. 2014. Special Issue on Free Energy. J. Chem. Theo. Comp. 10:2631-2631.

298. Maragliano, L., B. Roux, and E. Vanden-Eijnden. 2014. Comparison between Mean Forces and Swarms-of-Trajectories String Methods. J. Chem. Theo. Comp. 10:524-533.

297. Lin, Y. L., Y. Meng, L. Huang, and B. Roux. 2014. Computational Study of Gleevec and G6G Reveals Molecular Determinants of Kinase Inhibitor Selectivity. J. Am. Chem. Soc. 136:14753-14762.

296. Lin, Y. L., A. Aleksandrov, T. Simonson, and B. Roux. 2014. An Overview of Electrostatic Free Energy Computations for Solutions and Proteins. J. Chem. Theo. Comp. 10:2690-2709.

295. Li, Q., S. Wanderling, M. Paduch, D. Medovoy, A. Singharoy, R. McGreevy, C. A. Villalba-Galea, R. E. Hulse, B. Roux, K. Schulten, A. Kossiakoff, and E. Perozo. 2014. Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nat. Struct. Mol. Biol. 21:244-252.

294. Kazmier, K., S. Sharma, S. M. Islam, B. Roux, and H. S. McHaourab. 2014. Conformational cycle and ion-coupling mechanism of the Na+/hydantoin transporter Mhp1. Proc. Natl. Acad. Sci. U.S.A. 111:14752-14757.

293. Jo, S. W., X. Cheng, S. M. Islam, L. Huang, H. Rui, A. Zhu, H. S. Lee, Y. F. Qi, W. Han, K. Vanommeslaeghe, A. D. MacKerell, B. Roux, and W. Im. 2014. CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues. Adv Protein Chem Str 96:235-265.

292. Jiang, W., J. C. Phillips, L. Huang, M. Fajer, Y. Meng, J. C. Gumbart, Y. Luo, K. Schulten, and B. Roux. 2014. Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD. Computer physics communications 185:908-916.

291. Huang, J., P. E. Lopes, B. Roux, and A. D. MacKerell, Jr. 2014. Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model. J. Phys. Chem. Letters 5:3144-3150.

290. Horn, R., B. Roux, and J. Aqvist. 2014. Permeation redux: thermodynamics and kinetics of ion movement through potassium channels. Biophysical journal 106:1859-1863.

289. Gumbart, J. C., M. Beeby, G. J. Jensen, and B. Roux. 2014. Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations. PLoS computational biology 10:e1003475.

288. Das, A., M. Gur, M. H. Cheng, S. Jo, I. Bahar, and B. Roux. 2014. Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model. PLoS computational biology 10:e1003521.

287. Comer, J., B. Roux, and C. Chipot. 2014. Achieving ergodic sampling using replica-exchange free-energy calculations. Mol Simulat 40:218-228.

286. Chen, Y., and B. Roux. 2014. Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal. J. Chem. Phys. 141:114107.

285. Binkowski, T. A., W. Jiang, B. Roux, W. F. Anderson, and A. Joachimiak. 2014. Virtual high-throughput ligand screening. Methods Mol Biol 1140:251-261.

284. Adhikari, A. N., F. Bezanilla, B. Roux, and T. Sosnick. 2014. A computational framework for insertion of lanthanide-binding tags (LBT) in membrane proteins.

Back to the top



2013


283. Ziervogel, B. K., and B. Roux. 2013. The Binding of Antibiotics in OmpF Porin. Structure 21:76-87.

282. Yu, W., P. E. Lopes, B. Roux, and A. D. MacKerell, Jr. 2013. Six-site polarizable model of water based on the classical Drude oscillator. J. Chem. Phys. 138:034508.

281. Wojtas-Niziurski, W., Y. Meng, B. Roux, and S. Berneche. 2013. Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions. J. Chem. Theory Comp. 9:1885-1895.

280. Venable, R. M., Y. Luo, K. Gawrisch, B. Roux, and R. W. Pastor. 2013. Simulations of anionic lipid membranes: development of interaction-specific ion parameters and validation using NMR data. J. Phys. Chem. B 117:10183-10192.

279. Smith, J. C., and B. Roux. 2013. Eppur si muove! The 2013 nobel prize in chemistry. Structure 21:2102-2105.

278. Rowley, C. N., and B. Roux. 2013. A computational study of barium blockades in the KcsA potassium channel based on multi-ion potential of mean force calculations and free energy perturbation. J. Gen. Physiol. 142:451-463.

277. Roux, B., and J. Weare. 2013. On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method. J. Chem. Phys. B 138:084107.

276. Roux, B., and S. M. Islam. 2013. Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy. J. Phys. Chem. B 117:4733-4739.

275. Riahi, S., B. Roux, and C. N. Rowley. 2013. QM/MM Molecular Dynamics Simulations of the Hydration of Mg(II) and Zn(II) Ions. Can. J. Chem. 99:1-9.

274. Ostmeyer, J., S. Chakrapani, A. C. Pan, E. Perozo, and B. Roux. 2013. Recovery from Slow Inactivation in K+ Channels Controlled by Water Molecules Nature 501:121-124.

273. Luo, Y., W. Jiang, H. B. Yu, A. D. MacKerell, Jr., and B. Roux. 2013. Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field. Faraday Discussions 160:135-149.

272. Lopes, P. E., J. Huang, J. Shim, Y. Luo, H. Li, B. Roux, and A. D. Mackerell, Jr. 2013. Force Field for Peptides and Proteins based on the Classical Drude Oscillator. J. Chem. Theo. Comp. 9:5430-5449.

271. Lin, Y. L., and B. Roux. 2013. Computational Analysis of the Binding Specificity of Gleevec to Abl, c-Kit, Lck, and c-Src Tyrosine Kinases. J. Am. Chem. Soc. 135:14741-14753.

270. Lin, Y. L., Y. Meng, W. Jiang, and B. Roux. 2013. Explaining why Gleevec is a specific and potent inhibitor of Abl kinase. Proc. Natl. Acad. Sci. U.S.A. 110:1664-1669.

269. Lin, B., P. E. Lopes, B. Roux, and A. D. Mackerell, Jr. 2013. Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields. J. Chem. Phys. 139:084509.

268. Lau, A. Y., H. Salazar, L. Blachowicz, V. Ghisi, A. J. Plested, and B. Roux. 2013. A conformational intermediate in glutamate receptor activation. Neuron 79:492-503.

267. Khalili-Araghi, F., B. Ziervogel, J. C. Gumbart, and B. Roux. 2013. Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations. J. Gen. Physiol. 142:465-475.

266. Jo, S., W. Jiang, H. S. Lee, B. Roux, and W. Im. 2013. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application. J. Chem. Inf. Model 53:267-277.

265. Islam, S. M., R. A. Stein, H. S. McHaourab, and B. Roux. 2013. Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme. J. Phys. Chem. B 117:4740-4754.

264. Huang, L., and B. Roux. 2013. Automated Force Field Parameterization for Non-Polarizable and Polarizable Atomic Models Based on Target Data. J. Chem. Theo. Comp. 9.

263. Gumbart, J. C., I. Teo, B. Roux, and K. Schulten. 2013. Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion. J. Am. Chem. Soc. 135:2291-2297.

262. Gumbart, J. C., B. Roux, and C. Chipot. 2013. Standard binding free energies from computer simulations: What is the best strategy? J. Chem. Theo. Comp. 9:794-802.

261. Gumbart, J. C., B. Roux, and C. Chipot. 2013. Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles. J. Chem. Theo. Comp. 9:3789–3798.

260. Dhakshnamoorthy, B., B. Ziervogel, L. Blachowicz, and B. Roux. 2013. A Structural Study of Ion Permeation in OmpF Porin from Anomalous X-ray Diffraction and Molecular Dynamics Simulations. J. Am. Chem. Soc. 135:16561–16568.

259. Dama, J. F., A. V. Sinitskiy, M. McCullagh, J. Weare, B. Roux, A. R. Dinner, and G. A. Voth. 2013. The Theory of Ultra-Coarse-Graining. 1. General Principles. J. Chem. Theo. Comp. 9:2466–2480.

258. Chowdhary, J., E. Harder, P. E. Lopes, L. Huang, A. D. Mackerell, Jr., and B. Roux. 2013. A polarizable force field of dipalmitoylphosphatidylcholine based on the classical drude model for molecular dynamics simulations of lipids. J. Phys. Chem. B 117:9142-9160.

257. Bogdan, L., B. Roux, and S. Y. Noskov. 2013. Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations. J. Chem. Theo. Comp. 9:4165–4175.

256. Beeby, M., J. C. Gumbart, B. Roux, and G. J. Jensen. 2013. Architecture and assembly of the Gram-positive cell wall. Mol Microbiol 88:664-672.

Back to the top



2012


255. Yu, H., I. Ratheal, P. Artigas, and B. Roux. 2012. Molecular mechanisms of K+ selectivity in Na/K pump. Australian Journal of Chemistry 65:448-456.

254. Vargas, E., V. Yarov-Yarovoy, F. Khalili-Araghi, W. A. Catterall, M. L. Klein, M. Tarek, E. Lindahl, K. Schulten, E. Perozo, F. Bezanilla, and B. Roux. 2012. An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations. J. Gen. Physiol. 140:587-594.

253. Rowley, C. N., and B. Roux. 2012. The Solvation Structure of Na+ and K+ in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations. J. Chem. Theo. Comp. 8:3526−3535.

252. Roux, B. 2012. Comment on "Probing the Thermodynamics of Competitive Ion Binding Using Minimum Energy Structures". J. Phys. Chem. B.

251. Roux, B. 2012. Ion binding sites and their representations by reduced models. J. Phys. Chem. B 116:6966-6979.

250. Robertson, J. L., L. G. Palmer, and B. Roux. 2012. Multi-ion distributions in the cytoplasmic domain of inward rectifier potassium channels. Biophys. J. 103:434-443.

249. Raghuraman, H., J. F. Cordero-Morales, V. Jogini, A. C. Pan, A. Kollewe, B. Roux, and E. Perozo. 2012. Mechanism of Cd2+ coordination during slow inactivation in potassium channels. Structure 20:1332-1342.

248. Lee, K. I., S. Jo, H. Rui, B. Egwolf, B. Roux, R. W. Pastor, and W. Im. 2012. Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores. J Comput Chem 33:331-339.

247. Lacroix, J. J., S. A. Pless, L. Maragliano, F. V. Campos, J. D. Galpin, C. A. Ahern, B. Roux, and F. Bezanilla. 2012. Intermediate state trapping of a voltage sensor. J. Gen. Physiol. 140:635-652.

246. Kwon, T., B. Roux, S. Jo, J. B. Klauda, A. L. Harris, and T. A. Bargiello. 2012. Molecular dynamics simulations of the Cx26 hemichannel: insights into voltage-dependent loop-gating. Biophys. J. 102:1341-1351.

245. Khalili-Araghi, F., E. Tajkhorshid, B. Roux, and K. Schulten. 2012. Molecular dynamics investigation of the omega-current in the Kv1.2 voltage sensor domains. Biophys. J. 102:258-267.

244. Jiang, W., Y. Luo, L. Maragliano, and B. Roux. 2012. Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer. J. Chem. Theory Comput. 8:4672-4680.

243. Hyde, H. C., W. Sandtner, E. Vargas, A. T. Dagcan, J. L. Robertson, B. Roux, A. M. Correa, and F. Bezanilla. 2012. Nano-positioning system for structural analysis of functional homomeric proteins in multiple conformations. Structure 20:1629-1640.

242. Herrou, J., G. Rotskoff, Y. Luo, B. Roux, and S. Crosson. 2012. Structural basis of a protein partner switch that regulates the general stress response of alpha-proteobacteria. Proc. Natl. Acad. Sci. U.S.A. 109:E1415-1423.

241. Gumbart, J., and B. Roux. 2012. Determination of membrane-insertion free energies by molecular dynamics simulations. Biophys. J. 102:795-801.

240. Gumbart, J., F. Khalili-Araghi, M. Sotomayor, and B. Roux. 2012. Constant electric field simulations of the membrane potential illustrated with simple systems. Biochim. Biophys. Act. 1818:294-302.

Back to the top



2011


239. Yu, H., I. M. Ratheal, P. Artigas, and B. Roux. 2011. Protonation of key acidic residues is critical for the K-selectivity of the Na/K pump. Nat. Struct. & Mol. Biol. 18:1159-1163.

238. Yang, S., and B. Roux. 2011. EROS: Better than SAXS! Structure 19:3-4.

237. Vostrikov, V. V., H. Gu, H. I. Ingolfsson, J. F. Hinton, O. S. Andersen, B. Roux, and R. E. Koeppe, 2nd. 2011. Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. II: nuclear magnetic resonance experiments. J. Phys. Chem. B 115:7427-7432.

236. Vargas, E., F. Bezanilla, and B. Roux. 2011. In search of a consensus model of the resting state of a voltage-sensing domain. Neuron 72:713-720.

235. Sandtner, W., B. Egwolf, F. Khalili-Araghi, J. E. Sanchez-Rodriguez, B. Roux, F. Bezanilla, and M. Holmgren. 2011. Ouabain binding site in a functioning Na+/K+ ATPase. J. Biol. Chem. 286:38177-38183.

234. Roux, B., S. Berneche, B. Egwolf, B. Lev, S. Y. Noskov, C. N. Rowley, and H. Yu. 2011. Ion selectivity in channels and transporters. J. Gen. Physiol. 137:415-426.

233. Roux, B. 2011. Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail. Biophys. J. 101:755-756.

232. Pan, A. C., L. G. Cuello, E. Perozo, and B. Roux. 2011. Thermodynamic coupling between activation and inactivation gating in potassium channels revealed by free energy molecular dynamics simulations. J. Gen. Physiol. 138:571-580.

231. Luo, Y., E. Harder, R. S. Faibish, and B. Roux. 2011. Computer simulations of water flux and salt permeability of the reverse osmosis FT-30 aromatic polyamide membrane. J Membrane Sci 384:1-9.

230. Lau, A. Y., and B. Roux. 2011. The hidden energetics of ligand binding and activation in a glutamate receptor. Nat. Struct. Mol. Biol. 18:283-287.

229. Lau, A. Y., and B. Roux. 2011. Structural biology: One domain, multiple conformations. Nat. Chem. Biol. 7:130-131.

228. Jiang, W., D. J. Hardy, J. C. Phillips, A. D. Mackerell, Jr., K. Schulten, and B. Roux. 2011. High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. J Phys Chem Lett 2:87-92.

227. Ingolfsson, H. I., Y. Li, V. V. Vostrikov, H. Gu, J. F. Hinton, R. E. Koeppe, 2nd, B. Roux, and O. S. Andersen. 2011. Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. I: molecular dynamics simulations. J. Phys. Chem. B 115:7417-7426.

226. Gajewski, C., A. Dagcan, B. Roux, and C. Deutsch. 2011. Biogenesis of the pore architecture of a voltage-gated potassium channel. Proc. Natl. Acad. Sci. U.S.A. 108:3240-3245.

225. Chakrapani, S., J. F. Cordero-Morales, V. Jogini, A. C. Pan, D. M. Cortes, B. Roux, and E. Perozo. 2011. On the structural basis of modal gating behavior in K(+) channels. Nat. Struct. Mol. Biol. 18:67-74.

Back to the top



2008-2010


224. Yu, H., T. W. Whitfield, E. Harder, G. Lamoureux, I. Vorobyov, V. M. Anisimov, A. D. Mackerell, Jr., and B. Roux. 2010. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. J. Chem. Theory Comp. 6:774-786.

223. Yu, H., S. Y. Noskov, and B. Roux. 2010. Two mechanisms of ion selectivity in protein binding sites. Proc. Natl. Acad. Sci. U.S.A. 107:20329-20334.

222. Yu, H., C. L. Mazzanti, T. W. Whitfield, R. E. Koeppe, O. S. Andersen, and B. Roux. 2010. A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide. J. Am. Chem. Soc. 132:10847-10856.

221. Yang, S., M. Parisien, F. Major, and B. Roux. 2010. RNA structure determination using SAXS data. J. Phys. Chem. B 114:10039-10048.

220. Yang, S., L. Blachowicz, L. Makowski, and B. Roux. 2010. Multidomain assembled states of Hck tyrosine kinase in solution. Proc. Natl. Acad. Sci. U.S.A. 107:15757-15762.

219. Truchon, J. F., A. Nicholl's, J. A. Grant, R. I. Iftimie, B. Roux, and C. I. Bayly. 2010. Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions. J. Comput. Chem. 31:811-824.

218. Roux, B., and H. Yu. 2010. Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory. J. Chem. Phys. 132:234101.

217. Roux, B. 2010. Perspectives on: molecular dynamics and computational methods. J. Gen. Physiol. 135:547-548.

216. Roux, B. 2010. Exploring the ion selectivity properties of a large number of simplified binding site models. Biophys. J. 98:2877-2885.

215. Ratheal, I., G. Virgin, H. Yu, B. Roux, C. Gatto, and P. Artigas. 2010. Selectivity of externally facing ion binding sites in the Na/K pump to alkali metals and organic cations. Proc. Natl. Acad. Sci. U.S.A.

214. Luo, Y., and B. Roux. 2010. Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions J. Phys. Chem. Letters 1:183-189.

213. Luo, Y., B. Egwolf, D. E. Walters, and B. Roux. 2010. Ion selectivity of alpha-hemolysin with a beta-cyclodextrin adapter. I. Single ion potential of mean force and diffusion coefficient. J. Phys. Chem. B 114:952-958.

212. Li, Y., O. S. Andersen, and B. Roux. 2010. Energetics of double-ion occupancy in the gramicidin A channel. The journal of physical chemistry 114:13881-13888.

211. Khalili-Araghi, F., V. Jogini, V. Yarov-Yarovoy, E. Tajkhorshid, B. Roux, and K. Schulten. 2010. Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Biophys. J. 98:2189-2198.

210. Jiang, W., and B. Roux. 2010. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. J. Chem. Theory Comp. 6:2559-2565.

209. Ge, X., and B. Roux. 2010. Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome. The journal of physical chemistry 114:9525-9539.

208. Ge, X., and B. Roux. 2010. Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials. J Mol Recognit 23:128-141.

207. Egwolf, B., and B. Roux. 2010. Ion selectivity of the KcsA channel: a perspective from multi-ion free energy landscapes. J. Mol. Biol. 401:831-842.

206. Egwolf, B., Y. Luo, D. E. Walters, and B. Roux. 2010. Ion selectivity of alpha-hemolysin with beta-cyclodextrin adapter. II. Multi-ion effects studied with grand canonical Monte Carlo/Brownian dynamics simulations. J. Phys. Chem. B 114:2901-2909.

205. Dhakshnamoorthy, B., S. Raychaudhury, L. Blachowicz, and B. Roux. 2010. Cation-selective Pathway of OmpF Porin Revealed by Anomalous X-ray Diffraction. J. Mol. Biol. 396:293-300.

204. Dalmas, O., L. G. Cuello, V. Jogini, D. M. Cortes, B. Roux, and E. Perozo. 2010. Structural dynamics of the magnesium-bound conformation of CorA in a lipid bilayer. Structure 18:868-878.

203. Cuello, L. G., V. Jogini, D. M. Cortes, A. C. Pan, D. G. Gagnon, O. Dalmas, J. F. Cordero-Morales, S. Chakrapani, B. Roux, and E. Perozo. 2010. Structural basis for the coupling between activation and inactivation gates in K(+) channels. Nature 466:272-275.

202. Contreras, J. E., J. Chen, A. Y. Lau, V. Jogini, B. Roux, and M. Holmgren. 2010. Voltage profile along the permeation pathway of an open channel. Biophys. J. 99:2863-2869.

201. Chakrapani, S., P. Sompornpisut, P. Intharathep, B. Roux, and E. Perozo. 2010. The activated state of a sodium channel voltage sensor in a membrane environment. Proc. Natl. Acad. Sci. U.S.A. 107:5435-5440.

200. Baker, C. M., P. E. Lopes, X. Zhu, B. Roux, and A. D. Mackerell, Jr. 2010. Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. J. Chem. Theory Comput. 6:1181-1198.

199. Yu, H., and B. Roux. 2009. On the utilization of energy minimization to the study of ion selectivity. Biophys. J. 97:L15-17.

198. Yu, H., S. Y. Noskov, and B. Roux. 2009. Hydration number, topological control, and ion selectivity. J. Phys. Chem. B. 113:8725-8730.

197. Yang, S., S. Park, L. Makowski, and B. Roux. 2009. A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes. Biophys J 96:4449-4463.

196. Yang, S., N. K. Banavali, and B. Roux. 2009. Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Proc. Natl. Acad. Sci. U.S.A. 106:3776-3781.

195. Truchon, J. F., A. Nicholl's, B. Roux, R. I. Iftimie, and C. I. Bayly. 2009. Integrated Continuum Dielectric Approaches To Treat Molecular Polarizability and the Condensed Phase: Refractive Index and Implicit Solvation. J. Chem. Theo. Comp. 5:1785-1802

194. Tan, K., A. Sather, J. L. Robertson, S. Moy, B. Roux, and A. Joachimiak. 2009. Structure and electrostatic property of cytoplasmic domain of ZntB transporter. Protein Science 18:2043-2052.

193. Shivakumar, D., Y. Q. Deng, and B. Roux. 2009. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model. J. Chem. Theory Comp. 5:919-930.

192. Sezer, D., J. H. Freed, and B. Roux. 2009. Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations. J Am Chem Soc 131:2597-2605.

191. Park, S., J. P. Bardhan, B. Roux, and L. Makowski. 2009. Simulated x-ray scattering of protein solutions using explicit-solvent models. The Journal of chemical physics 130:134114.

190. Numano, R., S. Szobota, A. Y. Lau, P. Gorostiza, M. Volgraf, B. Roux, D. Trauner, and E. Y. Isacoff. 2009. Nanosculpting reversed wavelength sensitivity into a photoswitchable iGluR. Proc. Natl. Acad. Sci. U.S.A. 106:6814-6819.

189. Maragliano, L., E. Vanden-Eijnden, and B. Roux. 2009. Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials. . J. Chem. Theo. Comp. 5:2594-2589.

188. Lopes, P. E. M., B. Roux, and A. D. Mackerell, Jr. 2009. Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications. Theor Chem Acc 124:11-28.

187. Kollewe, A., A. Y. Lau, A. Sullivan, R. Benoit, and S. A. Goldstein. 2009. A structural model for K2P potassium channels based on 23 pairs of interacting sites and continuum electrostatics. J. Gen. Physiol. 134:53-68.

186. Jiang, W., M. Hodoscek, and B. Roux. 2009. Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD). J. Chem. Theory Comput. 5:2583-2588.

185. Harder, E., D. E. Walters, Y. D. Bodnar, R. S. Faibish, and B. Roux. 2009. Molecular Dynamics Study of a Polymeric Reverse Osmosis Membrane. The journal of physical chemistry 113:10177-10182.

184. Harder, E., A. D. Mackerell, Jr., and B. Roux. 2009. Many-body polarization effects and the membrane dipole potential. J Am Chem Soc 131:2760-2761.

183. Gan, W., S. Yang, and B. Roux. 2009. Atomistic view of the conformational activation of Src kinase using the string method with swarms-of-trajectories. Biophys J 97:L8-L10.

182. Gan, W., and B. Roux. 2009. Binding specificity of SH2 domains: insight from free energy simulations. Proteins 74:996-1007.

181. Freddolino, P. L., S. Park, B. Roux, and K. Schulten. 2009. Force field bias in protein folding simulations. Biophys J 96:3772-3780.

180. Deng, Y., and B. Roux. 2009. Computations of Standard Binding Free Energies with Molecular Dynamics Simulations. The journal of physical chemistry 113:2234–2246.

179. Brooks, B. R., C. L. Brooks, 3rd, A. D. Mackerell, Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, and M. Karplus. 2009. CHARMM: the biomolecular simulation program. J Comput Chem 30:1545-1614.

178. Banavali, N. K., and B. Roux. 2009. Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases. Proteins 74:378-389.

177. Yang, S., and B. Roux. 2008. Src kinase conformational activation: thermodynamics, pathways, and mechanisms. PLoS computational biology 4:e1000047.

176. Vasquez, V., M. Sotomayor, D. M. Cortes, B. Roux, K. Schulten, and E. Perozo. 2008. Three-dimensional architecture of membrane-embedded MscS in the closed conformation. J Mol Biol 378:55-70.

175. Truchon, J. F., A. Nicholl's, R. I. Iftimie, B. Roux, and C. I. Bayly. 2008. Accurate Molecular Polarizabilities Based on Continuum Electrostatics J. Chem. Theory Comput. 4:1480–1493

174. Sompornpisut, P., B. Roux, and E. Perozo. 2008. Structural refinement of membrane proteins by restrained molecular dynamics and solvent accessibility data. Biophys J 95:5349-5361.

173. Sezer, D., J. H. Freed, and B. Roux. 2008. 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 112:5755-5767.

172. Sezer, D., J. H. Freed, and B. Roux. 2008. Simulating electron spin resonance spectra of nitroxide spin labels from molecular dynamics and stochastic trajectories. The Journal of chemical physics 128:165106.

171. Sezer, D., J. H. Freed, and B. Roux. 2008. Using Markov models to simulate electron spin resonance spectra from molecular dynamics trajectories. The journal of physical chemistry 112:11014-11027.

170. Roux, B., O. S. Andersen, and T. W. Allen. 2008. 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 227102.

169. Roux, B. 2008. The membrane potential and its representation by a constant electric field in computer simulations. Biophys J 95:4205-4216.

168. Robertson, J. L., L. G. Palmer, and B. Roux. 2008. Long-pore electrostatics in inward-rectifier potassium channels. The Journal of general physiology 132:613-632.

167. Park, S., A. Y. Lau, and B. Roux. 2008. Computing conformational free energy by deactivated morphing. The Journal of chemical physics 129:134102.

166. Pan, A. C., D. Sezer, and B. Roux. 2008. Finding transition pathways using the string method with swarms of trajectories. The journal of physical chemistry 112:3432-3440.

165. Pan, A. C., and B. Roux. 2008. Building Markov state models along pathways to determine free energies and rates of transitions. The Journal of chemical physics 129:064107.

164. Noskov, S. Y., and B. Roux. 2008. Control of ion selectivity in LeuT: two Na+ binding sites with two different mechanisms. J Mol Biol 377:804-818.

163. Lewis, A., V. Jogini, L. Blachowicz, M. Laine, and B. Roux. 2008. Atomic constraints between the voltage sensor and the pore domain in a voltage-gated K+ channel of known structure. The Journal of general physiology 131:549-561.

162. Jo, S., M. Vargyas, J. Vasko-Szedlar, B. Roux, and W. Im. 2008. PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic acids research 36:W270-275.

161. Harder, E., and B. Roux. 2008. On the origin of the electrostatic potential difference at a liquid-vacuum interface. The Journal of chemical physics 129:234706.

160. Harder, E., V. M. Anisimov, T. Whitfield, A. D. MacKerell, Jr., and B. Roux. 2008. Understanding the dielectric properties of liquid amides from a polarizable force field. The journal of physical chemistry 112:3509-3521.

159. Deng, Y., and B. Roux. 2008. Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations. The Journal of chemical physics 128:115103.

Back to the top



2006-2007


158. Whitfield, T. W., S. Varma, E. Harder, G. Lamoureux, S. B. Rempe, and B. Roux. 2007. Theoretical study of aqueous solvation of K+ comparing ab initio, polarizable, and fixed-charge models. Journal of Chemical Theory and Computation 3:2068-2082.

157. Roux, B. 2007. A proton-controlled check valve for sodium ion transport. Nature Chemical Biology 3:609-610.

156. Roux, B. 2007. Lonely arginine seeks friendly environment. Journal of General Physiology 130:233-236.

155. Pathak, M. M., V. Yarov-Yarovoy, G. Agarwal, B. Roux, P. Barth, S. Kohout, F. Tombola, and E. Y. Isacoff. 2007. Closing in on the resting state of the shaker K+ channel. Neuron 56:124-140.

154. Noskov, S. Y., and B. Roux. 2007. Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels. Journal of General Physiology 129:135-143.

153. Lopes, P. E. M., G. Lamoureux, B. Roux, and A. D. Mackerell, Jr. 2007. Polarizable empirical force field for aromatic compounds based on the classical drude oscillator. Journal of Physical Chemistry B 111:2873-2885.

152. Lopes, P. E., G. Lamoureux, B. Roux, and A. D. Mackerell, Jr. 2007. Polarizable empirical force field for aromatic compounds based on the classical drude oscillator. J. Phys. Chem. B 111:2873-2885.

151. Lau, A. Y., and B. Roux. 2007. The free energy landscapes governing conformational changes in a glutamate receptor ligand-binding domain. Structure 15:1203-1214.

150. Jogini, V., and B. Roux. 2007. Dynamics of the Kv1.2 voltage-gated K+ channel in a membrane environment. Biophysical Journal 93:3070-3082.

149. Faraldo-Gomez, J. D., and B. Roux. 2007. Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: assessing entropic and environmental effects. Journal of Computational Chemistry 28:1634-1647.

148. Faraldo-Gomez, J. D., and B. Roux. 2007. On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases. Proc. Natl. Acad. Sci. U.S.A. 104:13643-13648.

147. Faraldo-Gomez, J. D., E. Kutluay, V. Jogini, Y. Zhao, L. Heginbotham, and B. Roux. 2007. 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 365:649-662.

146. Cordero-Morales, J. F., V. Jogini, A. Lewis, V. Vasquez, D. M. Cortes, B. Roux, and E. Perozo. 2007. Molecular driving forces determining potassium channel slow inactivation. Nature Structure and Molecular Biology 14:1062-1069.

145. Campos, F. V., B. Chanda, B. Roux, and F. Bezanilla. 2007. Two atomic constraints unambiguously position the S4 segment relative to S1 and S2 segments in the closed state of Shaker K channel. Proc. Natl. Acad. Sci. U.S.A. 104:7904-7909.

144. Banavali, N. K., and B. Roux. 2007. Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck. Proteins-Structure Function and Bioinformatics 67:1096-1112.

143. Anisimov, V. M., I. V. Vorobyov, B. Roux, and A. D. Mackerell, Jr. 2007. Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput 3:1927-1946.

142. Wang, J. Y., Y. Q. Deng, and B. Roux. 2006. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophysical Journal 91:2798-2814.

141. Roux, B. 2006. Dissecting the coupling between the voltage sensor and pore domains. Neuron 52:568-569.

140. Roux, B. 2006. Extracellular blockade of potassium channels by TEA(+): The tip of the iceberg? Journal of General Physiology 128:635-636.

139. Noskov, S. Y., and B. Roux. 2006. Ion selectivity in potassium channels. Biophysical Chemistry 124:279-291.

138. Murcia, M., J. D. Faraldo-Gomez, F. R. Maxfield, and B. Roux. 2006. Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol. Journal of Lipid Research 47:2614-2630.

137. Lamoureux, G., and B. Roux. 2006. Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field. The journal of physical chemistry 110:3308-3322.

136. Lamoureux, G., E. Harder, I. V. Vorobyov, B. Roux, and A. D. Mackerell, Jr. 2006. A polarizable model of water for molecular dynamics simulations of biomolecules. Chemical Physics Letters 418:245-249.

135. Harder, E., V. M. Anisimov, I. V. Vorobyov, P. E. M. Lopes, S. Y. Noskov, A. D. Mackerell, Jr., and B. Roux. 2006. 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.

134. Deng, Y. Q., and B. Roux. 2006. Calculation of standard binding free energies: Aromatic molecules in the T4 lysozyme L99A mutant. Journal of Chemical Theory and Computation 2:1255-1273.

133. Cordero-Morales, J. F., L. G. Cuello, Y. X. Zhao, V. Jogini, D. M. Cortes, B. Roux, and E. Perozo. 2006. Molecular determinants of gating at the potassium-channel selectivity filter. Nature Structural & Molecular Biology 13:311-318.

132. Allen, T. W., O. S. Andersen, and B. Roux. 2006. Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels. Biophysical Chemistry 124:251-267.

131. Allen, T. W., O. S. Andersen, and B. Roux. 2006. 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 90:3447-3468.

Back to the top



2004-2005


130. Woo, H. J., and B. Roux. 2005. Calculation of absolute protein-ligand binding free energy from computer simulations. Proc. Natl. Acad. Sci. U.S.A. 102:6825-6830.

129. Roux, B. 2005. The art of dissecting the function of a potassium channel. Neuron 47:777-778.

128. Roux, B. 2005. Ion conduction and selectivity in K+ channels. Annual Review of Biophysics and Biomolecular Structure 34:153-171.

127. Robertson, J. L., and B. Roux. 2005. One channel: Open and closed. Structure 13:1398-1400.

126. Noskov, S. Y., G. Lamoureux, and B. Roux. 2005. Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field. J. Phys. Chem. B 109:6705-6713.

125. Lagüe, P., B. Roux, and R. W. Pastor. 2005. Molecular dynamics simulations of the influenza hemagglutinin fusion peptide in micelles and bilayers: Conformational analysis of peptide and lipids. Journal of Molecular Biology 354:1129-1141.

124. Kutluay, E., B. Roux, and L. Heginbotham. 2005. Rapid intracellular TEA block of the KcsA potassium channel. Biophysical Journal 88:1018-1029.

123. Jogini, V., and B. Roux. 2005. Electrostatics of the intracellular vestibule of K+ channels. Journal of Molecular Biology 354:272-288.

122. Gilquin, B., S. Braud, M. A. L. Eriksson, B. Roux, T. D. Bailey, B. T. Priest, M. L. Garcia, A. Menez, and S. Gasparini. 2005. A variable residue in the pore of Kv1 channels is critical for the high affinity of Blockers from sea anemones and scorpions. Journal of Biological Chemistry 280:27093-27102.

121. Chanda, B., O. K. Asamoah, R. Blunck, B. Roux, and F. Bezanilla. 2005. Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement. Nature 436:852-856.

120. Berneche, S., and B. Roux. 2005. A gate in the selectivity filter of potassium channels. Structure 13:591-600.

119. Banavali, N. K., and B. Roux. 2005. The N-terminal end of the catalytic domain of Src kinase Hck is a conformational switch implicated in long-range allosteric regulation. Structure 13:1715-1723.

118. Banavali, N. K., and B. Roux. 2005. Free energy landscape of A-DNA to B-DNA conversion in aqueous solution. Journal of the American Chemical Society 127:6866-6876.

117. Anisimov, V. M., G. Lamoureux, I. V. Vorobyov, N. Huang, B. Roux, and A. D. Mackerell, Jr. 2005. Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator. Journal of Chemical Theory and Computation 1:153-168.

116. Andersen, O. S., R. E. Koeppe, and B. Roux. 2005. Gramicidin channels. Ieee Transactions on Nanobioscience 4:10-20.

115. Woo, H. J., A. R. Dinner, and B. Roux. 2004. Grand canonical Monte Carlo simulations of water in protein environments. Journal of Chemical Physics 121:6392-6400.

114. Roux, B., and K. Schulten. 2004. Computational studies of membrane channels. Structure 12:1343-1351.

113. Roux, B., T. Allen, S. Bernèche, and W. Im. 2004. Theoretical and computational models of biological ion channels. Quarterly Reviews of Biophysics 37:15-103.

112. Noskov, S. Y., W. Im, and B. Roux. 2004. Ion permeation through the alpha-hemolysin channel: Theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory. Biophysical Journal 87:2299-2309.

111. Noskov, S. Y., S. Bernèche, and B. Roux. 2004. Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431:830-834.

110. Laine, M., D. M. Papazian, and B. Roux. 2004. Critical assessment of a proposed model of Shaker. Febs Letters 564:257-263.

109. Faraldo-Gomez, J. D., and B. Roux. 2004. Electrostatics of ion stabilization in a ClC chloride channel homologue from Escherichia coli. Journal of Molecular Biology 339:981-1000.

108. Deng, Y. Q., and B. Roux. 2004. Hydration of amino acid side chains: Nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules. Journal of Physical Chemistry B 108:16567-16576.

107. Chakrabarti, N., E. Tajkhorshid, B. Roux, and R. Pomès. 2004. Molecular basis of proton blockage in aquaporins. Structure 12:65-74.

106. Chakrabarti, N., B. Roux, and R. Pomès. 2004. Structural determinants of proton blockage in aquaporins. Journal of Molecular Biology 343:493-510.

Back to the top



2000-2003


103. Silverman, W. R., B. Roux, and D. M. Papazian. 2003. Structural basis of two-stage voltage-dependent activation in K+ channels. Proc. Natl. Acad. Sci. U.S.A. 100:2935-2940.

102. Lamoureux, G., and B. Roux. 2003. Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm. J. Chem. Phys. 119:3025-3039.

101. Lamoureux, G., A. D. Mackerell, Jr., and B. Roux. 2003. A simple polarizable model of water based on classical Drude oscillators. J. Chem. Phys. 119:5185-5197.

100. Laine, M., M. C. A. Lin, J. P. A. Bannister, W. R. Silverman, A. F. Mock, B. Roux, and D. M. Papazian. 2003. Atomic proximity between S4 segment and pore domain in Shaker potassium channels. Neuron 39:467-481.

99. Bernèche, S., and B. Roux. 2003. A microscopic view of ion conduction through the K+ channel. Proc. Natl. Acad. Sci. U.S.A. 100:8644-8648.

98. Allen, T. W., O. S. Andersen, and B. Roux. 2003. 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 125:9868-9877.

97. Yang, L. J., W. A. Beard, S. H. Wilson, B. Roux, S. Broyde, and T. Schlick. 2002. Local deformations revealed by dynamics simulations of DNA polymerase beta with DNA mismatches at the primer terminus. Journal of Molecular Biology 321:459-478.

96. Simoes, M., L. Garneau, H. Klein, U. Banderali, F. Hobeila, B. Roux, L. Parent, and R. Sauve. 2002. Cysteine mutagenesis and computer modeling of the S6 region of an intermediate conductance IKCa channel. Journal of General Physiology 120:99-116.

95. Roux, B., and S. Bernèche. 2002. On the potential functions used in molecular dynamics simulations of ion channels. Biophysical Journal 82:1681-1684.

94. Roux, B. 2002. What can be deduced about the structure of Shaker from available data? Ion Channels: From Atomic Resolution Physiology to Functional Genomics 245:84-108.

93. Roux, B. 2002. Computational studies of the gramicidin channel. Accounts of Chemical Research 35:366-375.

92. Roux, B. 2002. Theoretical and computational models of ion channels. Current Opinion in Structural Biology 12:182-189.

91. Pomès, R., and B. Roux. 2002. Molecular mechanism of H+ conduction in the single-file water chain of the gramicidin channel. Biophysical Journal 82:2304-2316.

90. Philippsen, A., W. P. Im, A. Engel, T. Schirmer, B. Roux, and D. J. Muller. 2002. Imaging the electrostatic potential of transmembrane channels: Atomic probe microscopy of OmpF porin. Biophysical Journal 82:1667-1676.

89. Parent, L., M. Sauve, S. Bernèche, and B. Roux. 2002. Ion conduction through the K+ channel. M S-Medecine Sciences 18:605-609.

88. Im, W., and B. Roux. 2002. Ion permeation and selectivity of OmpF porin: A theoretical study based on molecular dynamics, brownian dynamics, and continuum electrodiffusion theory. Journal of Molecular Biology 322:851-869.

87. Im, W., and B. Roux. 2002. 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 319:1177-1197.

86. Eriksson, M. A. L., and B. Roux. 2002. 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 83:2595-2609.

85. Bernèche, S., and B. Roux. 2002. The ionization state and the conformation of Glu-71 in the KcsA K+ channel. Biophysical Journal 82:772-780.

84. Banavali, N. K., and B. Roux. 2002. Atomic radii for continuum electrostatics calculations on nucleic acids. Journal of Physical Chemistry B 106:11026-11035.

83. Banavali, N. K., W. Im, and B. Roux. 2002. Electrostatic free energy calculations using the generalized solvent boundary potential method. Journal of Chemical Physics 117:7381-7388.

82. Young, M. A., S. Gonfloni, G. Superti-Furga, B. Roux, and J. Kuriyan. 2001. Dynamic coupling between the SH2 and SH3 domains of c-Src and hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell 105:115-126.

81. Souaille, M., and B. Roux. 2001. Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations. Computer Physics Communications 135:40-57.

80. Schumaker, M. F., R. Pomès, and B. Roux. 2001. Framework model for single proton conduction through gramicidin. Biophysical Journal 80:12-30.

79. Roux, B., J. Y. Lapointe, and D. G. Bichet. 2001. Permeation by water but not protons through aquaporin-1: structural analysis. M S-Medecine Sciences 17:115-116.

78. Lagüe, P., M. J. Zuckermann, and B. Roux. 2001. Lipid-mediated interactions between intrinsic membrane proteins: Dependence on protein size and lipid composition. Biophysical Journal 81:276-284.

77. Im, W., and B. Roux. 2001. Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry. Journal of Chemical Physics 115:4850-4861.

76. Im, W., S. Bernèche, and B. Roux. 2001. Generalized solvent boundary potential for computer simulations. Journal of Chemical Physics 114:2924-2937.

75. Crouzy, S., S. Bernèche, and B. Roux. 2001. Extracellular blockade of K+ channels by TEA: Results from molecular dynamics simulations of the KcsA channel. Journal of General Physiology 118:207-217.

74. Bernèche, S., and B. Roux. 2001. Energetics of ion conduction through the K+ channel. Nature 414:73-77.

73. Shobana, S., B. Roux, and O. S. Andersen. 2000. Free energy simulations: Thermodynamic reversibility and variability. Journal of Physical Chemistry B 104:5179-5190.

72. Schumaker, M. F., R. Pomès, and B. Roux. 2000. A combined molecular dynamics and diffusion model of single proton conduction through gramicidin. Biophysical Journal 79:2840-2857.

71. Roux, B., S. Bernèche, and W. Im. 2000. Ion channels, permeation, and electrostatics: Insight into the function of KcsA. Biochemistry 39:13295-13306.

70. Nina, M., S. Bernèche, and B. Roux. 2000. Anchoring of a monotopic membrane protein: the binding of prostaglandin H-2 synthase-1 to the surface of a phospholipid bilayer. European Biophysics Journal with Biophysics Letters 29:439-454.

69. Lagüe, P., M. J. Zuckermann, and B. Roux. 2000. Lipid-mediated interactions between intrinsic membrane proteins: A theoretical study based on integral equations. Biophysical Journal 79:2867-2879.

68. Im, W., S. Seefeld, and B. Roux. 2000. A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. Biophysical Journal 79:788-801.

67. Du, Q. H., D. Beglov, and B. Roux. 2000. Solvation free energy of polar and nonpolar molecules in water: An extended interaction site integral equation theory in three dimensions. Journal of Physical Chemistry B 104:796-805.

66. Bernèche, S., and B. Roux. 2000. Molecular dynamics of the KcsA K+ channel in a bilayer membrane. Biophysical Journal 78:2900-2917.

Back to the top



1997-1999


65. Roux, B., and T. Simonson. 1999. Implicit solvent models. Biophysical Chemistry 78:1-20.

64. Roux, B., and R. MacKinnon. 1999. The cavity and pore helices the KcsA K+ channel: Electrostatic stabilization of monovalent cations. Science 285:100-102.

63. Roux, B. 1999. Statistical mechanical equilibrium theory of selective ion channels. Biophysical Journal 77:139-153.

62. Roux, B. 1999. Theories of ion permeation: A chaser. Journal of General Physiology 114:605-608.

61. Roux, B. 1999. Proton wires are different. Biophysical Journal 77:2331-2332.

60. Pomès, R., E. Eisenmesser, C. B. Post, and B. Roux. 1999. Calculating excess chemical potentials using dynamic simulations in the fourth dimension. Journal of Chemical Physics 111:3387-3395.

59. Nina, M., W. Im, and B. Roux. 1999. Optimized atomic radii for protein continuum electrostatics solvation forces. Biophysical Chemistry 78:89-96.

58. Crouzy, S., J. Baudry, J. C. Smith, and B. Roux. 1999. 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.

57. Baudry, J., S. Crouzy, B. Roux, and J. C. Smith. 1999. Simulation analysis of the retinal conformational equilibrium in dark-adapted bacteriorhodopsin. Biophysical Journal 76:1909-1917.

56. Roux, B. 1998. Molecular dynamics simulations of ion channels: How far have we gone and where are we heading? Biophysical Journal 74:2744-2745.

55. Pomès, R., and B. Roux. 1998. Free energy profiles for H+ conduction along hydrogen-bonded chains of water molecules. Biophysical Journal 75:33-40.

54. Marchand, S., and B. Roux. 1998. Molecular dynamics study of calbindin D-9k in the apo and singly and doubly calcium-loaded states. Proteins-Structure Function and Genetics 33:265-284.

53. Mackerell, A. D., Jr., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 102:3586-3616.

52. Lagüe, P., M. J. Zuckermann, and B. Roux. 1998. Protein inclusion in lipid membranes: A theory based on the hypernetted chain integral equation. Faraday Discussions:165-172.

51. Im, W., D. Beglov, and B. Roux. 1998. Continuum Solvation Model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Computer Physics Communications 111:59-75.

50. Chakrabarti, N., T. Carrington, and B. Roux. 1998. Rate constants in quantum mechanical systems: A rigorous and practical path-integral formulation for computer simulations. Chemical Physics Letters 293:209-220.

49. Bernèche, S., M. Nina, and B. Roux. 1998. Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane. Biophysical Journal 75:1603-1618.

48. Woolf, T. B., and B. Roux. 1997. The binding site of sodium in the gramicidin A channel: Comparison of molecular dynamics with solid-state NMR data. Biophysical Journal 72:1930-1945.

47. Sharafeddin, O. A., K. Hinsen, T. Carrington, and B. Roux. 1997. Mixing quantum-classical molecular dynamics methods applied to intramolecular proton transfer in acetylacetone. Journal of Computational Chemistry 18:1760-1772.

46. Roux, B. 1997. Influence of the membrane potential on the free energy of an intrinsic protein. Biophysical Journal 73:2980-2989.

45. Nina, M., D. Beglov, and B. Roux. 1997. Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations. Journal of Physical Chemistry B 101:5239-5248.

44. Mohanty, D., R. Elber, D. Thirumalai, D. Beglov, and B. Roux. 1997. Kinetics of peptide folding: Computer simulations of SYPFDV and peptide variants in water. Journal of Molecular Biology 272:423-442.

43. Ketchem, R. R., B. Roux, and T. A. Cross. 1997. High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints. Structure 5:1655-1669.

42. Hinsen, K., and B. Roux. 1997. A potential function for computer simulation studies of proton transfer in acetylacetone. Journal of Computational Chemistry 18:368-380.

41. Hinsen, K., and B. Roux. 1997. Potential of mean force and reaction rates for proton transfer in acetylacetone. Journal of Chemical Physics 106:3567-3577.

40. Gambu, I., and B. Roux. 1997. Interaction of K+ with a phospholipid bilayer: A molecular dynamics study. Journal of Physical Chemistry B 101:6066-6072.

39. Belohorcova, K., J. H. Davis, T. B. Woolf, and B. Roux. 1997. Structure and dynamics of an amphiphilic peptide in a lipid bilayer: A molecular dynamics study. Biophysical Journal 73:3039-3055.

38. Beglov, D., and B. Roux. 1997. An integral equation to describe the solvation of polar molecules in liquid water. Journal of Physical Chemistry B 101:7821-7826.

37. Baudry, J., S. Crouzy, B. Roux, and J. C. Smith. 1997. Quantum chemical and free energy simulation analysis of retinal conformational energetics. Journal of Chemical Information and Computer Sciences 37:1018-1024.

Back to the top



1985-1996


36. Woolf, T. B., and B. Roux. 1996. Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer. Proteins-Structure Function and Genetics 24:92-114.

35. Roux, B., M. Nina, R. Pomès, and J. C. Smith. 1996. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: A molecular dynamics free energy perturbation study. Biophysical Journal 71:670-681.

34. Roux, B. 1996. Commentary: Surface tension of biomembranes. Biophysical Journal 71:1346-1347.

33. Roux, B. 1996. Valence selectivity of the gramicidin channel: A molecular dynamics free energy perturbation study. Biophysical Journal 71:3177-3185.

32. Pomès, R., and B. Roux. 1996. Theoretical study of H+ translocation along a model proton wire. Journal of Physical Chemistry 100:2519-2527.

31. Pomès, R., and B. Roux. 1996. 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.

30. Petit, J. M., B. Roux, X. X. Zhu, and P. M. Macdonald. 1996. A new physical model for the diffusion of solvents and solute probes in polymer solutions. Macromolecules 29:6031-6036.

29. Beglov, D., and B. Roux. 1996. Solvation of complex molecules in a polar liquid: An integral equation theory. Journal of Chemical Physics 104:8678-8689.

28. Woolf, T. B., V. G. Malkin, O. L. Malkina, D. R. Salahub, and B. Roux. 1995. The Backbone N-15 Chemical-Shift Tensor of the Gramicidin Channel - a Molecular-Dynamics and Density-Functional Study. Chemical Physics Letters 239:186-194.

27. Roux, B., B. Prodhom, and M. Karplus. 1995. Ion-Transport in the Gramicidin Channel - Molecular-Dynamics Study of Single and Double Occupancy. Biophysical Journal 68:876-892.

26. Roux, B., and M. Karplus. 1995. Potential-Energy Function for Cation-Peptide Interactions - an Ab-Initio Study. Journal of Computational Chemistry 16:690-704.

25. Roux, B. 1995. The Calculation of the Potential of Mean Force Using Computer-Simulations. Computer Physics Communications 91:275-282.

24. Pomès, R., and B. Roux. 1995. Quantum Effects on the Structure and Energy of a Protonated Linear-Chain of Hydrogen-Bonded Water-Molecules. Chemical Physics Letters 234:416-424.

23. Nina, M., B. Roux, and J. C. Smith. 1995. Functional Interactions in Bacteriorhodopsin - a Theoretical-Analysis of Retinal Hydrogen-Bonding with Water. Biophysical Journal 68:25-39.

22. Beglov, D., and B. Roux. 1995. Dominant Solvation Effects from the Primary Shell of Hydration - Approximation for Molecular-Dynamics Simulations. Biopolymers 35:171-178.

21. Beglov, D., and B. Roux. 1995. Numerical-Solution of the Hypernetted-Chain Equation for a Solute of Arbitrary Geometry in 3 Dimensions. Journal of Chemical Physics 103:360-364.

20. Woolf, T. B., and B. Roux. 1994. Conformational Flexibility of O-Phosphorylcholine and O-Phosphorylethanolamine - a Molecular-Dynamics Study of Solvation Effects. Journal of the American Chemical Society 116:5916-5926.

19. Woolf, T. B., and B. Roux. 1994. Molecular-Dynamics Simulation of the Gramicidin Channel in a Phospholipid-Bilayer. Proc. Natl. Acad. Sci. U.S.A. 91:11631-11635.

18. Roux, B., and M. Karplus. 1994. Molecular-Dynamics Simulations of the Gramicidin Channel. Annual Review of Biophysics and Biomolecular Structure 23:731-761.

17. Crouzy, S., T. B. Woolf, and B. Roux. 1994. A Molecular-Dynamics Study of Gating in Dioxolane-Linked Gramicidin-a Channels. Biophysical Journal 67:1370-1386.

16. Beglov, D., and B. Roux. 1994. Finite Representation of an Infinite Bulk System - Solvent Boundary Potential for Computer-Simulations. Journal of Chemical Physics 100:9050-9063.

15. Thomas, A., B. Roux, and J. C. Smith. 1993. Computer-Simulations of the Flexibility of a Series of Synthetic Cyclic Peptide Analogs. Biopolymers 33:1249-1270.

14. Roux, B., and M. Karplus. 1993. 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.

13. Roux, B. 1993. Nonadditivity in Cation Peptide Interactions - a Molecular-Dynamics and Ab-Initio Study of Na+ in the Gramicidin Channel. Chemical Physics Letters 212:231-240.

12. Nina, M., J. C. Smith, and B. Roux. 1993. Ab-Initio Quantum-Chemical Analysis of Schiff-Base Water Interactions in Bacteriorhodopsin. Theochem-Journal of Molecular Structure 105:231-245.

11. Ferrand, M., G. Zaccai, M. Nina, J. C. Smith, C. Etchebest, and B. Roux. 1993. Structure and Dynamics of Bacteriorhodopsin - Comparison of Simulation and Experiment. Febs Letters 327:256-260.

10. Calmettes, P., B. Roux, D. Durand, M. Desmadril, and J. C. Smith. 1993. Configurational Distribution of Denatured Phosphoglycerate Kinase. Journal of Molecular Biology 231:840-848.

9. Bruschweiler, R., B. Roux, M. Blackledge, C. Griesinger, M. Karplus, and R. R. Ernst. 1992. 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.

8. Roux, B., and M. Karplus. 1991. Ion-Transport in a Model Gramicidin Channel - Structure and Thermodynamics. Biophysical Journal 59:961-981.

7. Roux, B., and M. Karplus. 1991. Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility. Journal of Physical Chemistry 95:4856-4868.

6. Yu, H. A., B. Roux, and M. Karplus. 1990. Solvation Thermodynamics - an Approach from Analytic Temperature Derivatives. Journal of Chemical Physics 92:5020-5032.

5. Straub, J. E., B. J. Berne, and B. Roux. 1990. Spatial Dependence of Time-Dependent Friction for Pair Diffusion in a Simple Fluid. Journal of Chemical Physics 93:6804-6812.

4. Roux, B., H. A. Yu, and M. Karplus. 1990. Molecular-Basis for the Born Model of Ion Solvation. Journal of Physical Chemistry 94:4683-4688.

3. Roux, B., R. Bruschweiler, and R. R. Ernst. 1990. The Structure of Gramicidin-a in Dimethylsulfoxide Acetone. European Journal of Biochemistry 194:57-60.

2. Roux, B., and M. Karplus. 1988. The Normal-Modes of the Gramicidin-a Dimer Channel. Biophysical Journal 53:297-309.

1. Roux, B., and R. Sauvé. 1985. A General-Solution to the Time Interval Omission Problem Applied to Single Channel Analysis. Biophysical Journal 48:149-158.

Back to the top