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Items: 1 to 50 of 539

1.

Shifts in the selectivity filter dynamics cause modal gating in K+ channels.

Jekhmane S, Medeiros-Silva J, Li J, Kümmerer F, Müller-Hermes C, Baldus M, Roux B, Weingarth M.

Nat Commun. 2019 Jan 10;10(1):123. doi: 10.1038/s41467-018-07973-6.

2.

[Hepatocarcinoma: breath or ferment].

Roux B, Noyau L, Julien B.

Med Sci (Paris). 2018 Dec;34(12):1107-1109. doi: 10.1051/medsci/2018303. Epub 2019 Jan 9. French. No abstract available.

PMID:
30623768
3.

Long Non-coding RNAs Are Central Regulators of the IL-1β-Induced Inflammatory Response in Normal and Idiopathic Pulmonary Lung Fibroblasts.

Hadjicharalambous MR, Roux BT, Feghali-Bostwick CA, Murray LA, Clarke DL, Lindsay MA.

Front Immunol. 2018 Dec 11;9:2906. doi: 10.3389/fimmu.2018.02906. eCollection 2018.

4.

Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg2+".

Villa F, MacKerell AD Jr, Roux B, Simonson T.

J Phys Chem A. 2019 Jan 2. doi: 10.1021/acs.jpca.8b12337. [Epub ahead of print] No abstract available.

PMID:
30600990
5.

Proton Countertransport and Coupled Gating in the Sarcoplasmic Reticulum Calcium Pump.

Rui H, Das A, Nakamoto R, Roux B.

J Mol Biol. 2018 Dec 7;430(24):5050-5065. doi: 10.1016/j.jmb.2018.10.014. Epub 2018 Oct 26.

PMID:
30539761
6.

Nutritional management of young infants presenting with acute bronchiolitis in Belgium, France and Switzerland: survey of current practices and documentary search of national guidelines worldwide.

Valla FV, Baudin F, Demaret P, Rooze S, Moullet C, Cotting J, Ford-Chessel C, Pouyau R, Peretti N, Tume LN, Milesi C, Le Roux BG.

Eur J Pediatr. 2018 Dec 1. doi: 10.1007/s00431-018-3300-1. [Epub ahead of print]

PMID:
30506396
7.

Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B.

J Chem Theory Comput. 2018 Nov 27. doi: 10.1021/acs.jctc.8b01075. [Epub ahead of print] No abstract available.

PMID:
30480445
8.

Molecular Dynamics of Ion Conduction through the Selectivity Filter of the NaVAb Sodium Channel.

Callahan KM, Roux B.

J Phys Chem B. 2018 Nov 8;122(44):10126-10142. doi: 10.1021/acs.jpcb.8b09678. Epub 2018 Oct 29.

PMID:
30351118
9.

Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages.

Loeffler HH, Bosisio S, Duarte Ramos Matos G, Suh D, Roux B, Mobley DL, Michel J.

J Chem Theory Comput. 2018 Nov 13;14(11):5567-5582. doi: 10.1021/acs.jctc.8b00544. Epub 2018 Oct 22.

PMID:
30289712
10.

Amphiphile-Induced Phase Transition of Liquid Crystals at Aqueous Interfaces.

Ramezani-Dakhel H, Rahimi M, Pendery J, Kim YK, Thayumanavan S, Roux B, Abbott NL, de Pablo JJ.

ACS Appl Mater Interfaces. 2018 Oct 31;10(43):37618-37624. doi: 10.1021/acsami.8b09639. Epub 2018 Oct 22.

PMID:
30285408
11.

1H, 15N, and 13C resonance assignments of the intrinsically disordered SH4 and Unique domains of Hck.

Pond MP, Blachowicz L, Roux B.

Biomol NMR Assign. 2018 Oct 4. doi: 10.1007/s12104-018-9854-z. [Epub ahead of print]

PMID:
30284668
12.

Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis.

Jiang W, Thirman J, Jo S, Roux B.

J Phys Chem B. 2018 Oct 18;122(41):9435-9442. doi: 10.1021/acs.jpcb.8b03277. Epub 2018 Oct 3.

PMID:
30253098
13.

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.

Meng Y, Ahuja LG, Kornev AP, Taylor SS, Roux B.

J Mol Biol. 2018 Oct 19;430(21):4439. doi: 10.1016/j.jmb.2018.09.001. Epub 2018 Sep 13. No abstract available.

PMID:
30220583
14.

A generalized linear response framework for expanded ensemble and replica exchange simulations.

Radak BK, Suh D, Roux B.

J Chem Phys. 2018 Aug 21;149(7):072315. doi: 10.1063/1.5027494.

PMID:
30134700
15.

Rapid constriction of the selectivity filter underlies C-type inactivation in the KcsA potassium channel.

Li J, Ostmeyer J, Cuello LG, Perozo E, Roux B.

J Gen Physiol. 2018 Oct 1;150(10):1408-1420. doi: 10.1085/jgp.201812082. Epub 2018 Aug 2.

PMID:
30072373
16.

Laser Capture Micro-Dissection Coupled to RNA Sequencing: A Powerful Approach Applied to the Model Legume Medicago truncatula in Interaction with Sinorhizobium meliloti.

Roux B, Rodde N, Moreau S, Jardinaud MF, Gamas P.

Methods Mol Biol. 2018;1830:191-224. doi: 10.1007/978-1-4939-8657-6_12.

PMID:
30043372
17.

Preformed Vascular Networks Survive and Enhance Vascularization in Critical Sized Cranial Defects.

Roux BM, Akar B, Zhou W, Stojkova K, Barrera B, Brankov J, Brey EM.

Tissue Eng Part A. 2018 Nov;24(21-22):1603-1615. doi: 10.1089/ten.TEA.2017.0493. Epub 2018 Oct 12.

PMID:
30019616
18.

Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg2.

Villa F, MacKerell AD Jr, Roux B, Simonson T.

J Phys Chem A. 2018 Jul 26;122(29):6147-6155. doi: 10.1021/acs.jpca.8b04418. Epub 2018 Jul 18.

PMID:
29966419
19.

Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.

Aleksandrov A, Lin FY, Roux B, MacKerell AD Jr.

J Comput Chem. 2018 Aug 15;39(22):1707-1719. doi: 10.1002/jcc.25345. Epub 2018 May 8.

PMID:
29737546
20.

Optimized Lennard-Jones Parameters for Druglike Small Molecules.

Boulanger E, Huang L, Rupakheti C, MacKerell AD Jr, Roux B.

J Chem Theory Comput. 2018 Jun 12;14(6):3121-3131. doi: 10.1021/acs.jctc.8b00172. Epub 2018 May 7.

21.

The unique functioning of a pre-Columbian Amazonian floodplain fishery.

Blatrix R, Roux B, Béarez P, Prestes-Carneiro G, Amaya M, Aramayo JL, Rodrigues L, Lombardo U, Iriarte J, de Souza JG, Robinson M, Bernard C, Pouilly M, Durécu M, Huchzermeyer CF, Kalebe M, Ovando A, McKey D.

Sci Rep. 2018 Apr 16;8(1):5998. doi: 10.1038/s41598-018-24454-4.

22.

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.

Lin FY, Lopes PEM, Harder E, Roux B, MacKerell AD Jr.

J Chem Inf Model. 2018 May 29;58(5):993-1004. doi: 10.1021/acs.jcim.8b00132. Epub 2018 Apr 17.

PMID:
29624370
23.

Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models.

Meng Y, Gao C, Clawson DK, Atwell S, Russell M, Vieth M, Roux B.

J Chem Theory Comput. 2018 May 8;14(5):2721-2732. doi: 10.1021/acs.jctc.7b01170. Epub 2018 Apr 3.

24.

A Catalytically Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation.

Meng Y, Ahuja LG, Kornev AP, Taylor SS, Roux B.

J Mol Biol. 2018 Mar 16;430(6):881-889. doi: 10.1016/j.jmb.2018.01.019. Epub 2018 Feb 2. Erratum in: J Mol Biol. 2018 Oct 19;430(21):4439.

PMID:
29410316
25.

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator.

Suh D, Radak BK, Chipot C, Roux B.

J Chem Phys. 2018 Jan 7;148(1):014101. doi: 10.1063/1.5004154.

PMID:
29306299
26.

Water Flux Induced Reorientation of Liquid Crystals.

Ramezani-Dakhel H, Sadati M, Zhang R, Rahimi M, Kurtenbach K, Roux B, de Pablo JJ.

ACS Cent Sci. 2017 Dec 27;3(12):1345-1349. doi: 10.1021/acscentsci.7b00495. Epub 2017 Dec 15.

27.

Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions.

Han K, Venable RM, Bryant AM, Legacy CJ, Shen R, Li H, Roux B, Gericke A, Pastor RW.

J Phys Chem B. 2018 Feb 1;122(4):1484-1494. doi: 10.1021/acs.jpcb.7b10730. Epub 2018 Jan 22.

PMID:
29293344
28.

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B.

J Chem Theory Comput. 2017 Dec 12;13(12):5933-5944. doi: 10.1021/acs.jctc.7b00875. Epub 2017 Nov 22.

29.

Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for C-type inactivation.

Li J, Ostmeyer J, Boulanger E, Rui H, Perozo E, Roux B.

Proc Natl Acad Sci U S A. 2017 Oct 17;114(42):11145-11150. doi: 10.1073/pnas.1706983114. Epub 2017 Oct 2.

30.

New Coarse Variables for the Accurate Determination of Standard Binding Free Energies.

Fu H, Cai W, Hénin J, Roux B, Chipot C.

J Chem Theory Comput. 2017 Nov 14;13(11):5173-5178. doi: 10.1021/acs.jctc.7b00791. Epub 2017 Oct 9.

PMID:
28965398
31.

The Role of Ubiquitination and Hepatocyte Growth Factor-Regulated Tyrosine Kinase Substrate in the Degradation of the Adrenomedullin Type I Receptor.

Roux BT, Bauer CC, McNeish AJ, Ward SG, Cottrell GS.

Sci Rep. 2017 Sep 28;7(1):12389. doi: 10.1038/s41598-017-12585-z.

32.

Catalog of Differentially Expressed Long Non-Coding RNA following Activation of Human and Mouse Innate Immune Response.

Roux BT, Heward JA, Donnelly LE, Jones SW, Lindsay MA.

Front Immunol. 2017 Aug 29;8:1038. doi: 10.3389/fimmu.2017.01038. eCollection 2017.

33.

Management of oral bisphosphonates treatment by rheumatologists and determinants of therapeutic changes: a case-vignette-based study.

Roux C, Baron G, Briot K, Roux B, Cortet B, Thomas T.

Osteoporos Int. 2017 Dec;28(12):3339-3345. doi: 10.1007/s00198-017-4188-8. Epub 2017 Aug 29.

PMID:
28852785
34.

Transcriptional profiling identifies differential expression of long non-coding RNAs in Jo-1 associated and inclusion body myositis.

Hamann PD, Roux BT, Heward JA, Love S, McHugh NJ, Jones SW, Lindsay MA.

Sci Rep. 2017 Aug 14;7(1):8024. doi: 10.1038/s41598-017-08603-9.

35.

Phosphoantigen-induced conformational change of butyrophilin 3A1 (BTN3A1) and its implication on Vγ9Vδ2 T cell activation.

Gu S, Sachleben JR, Boughter CT, Nawrocka WI, Borowska MT, Tarrasch JT, Skiniotis G, Roux B, Adams EJ.

Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):E7311-E7320. doi: 10.1073/pnas.1707547114. Epub 2017 Aug 14.

36.

Machine Learning Force Field Parameters from Ab Initio Data.

Li Y, Li H, Pickard FC 4th, Narayanan B, Sen FG, Chan MKY, Sankaranarayanan SKRS, Brooks BR, Roux B.

J Chem Theory Comput. 2017 Sep 12;13(9):4492-4503. doi: 10.1021/acs.jctc.7b00521. Epub 2017 Sep 1.

37.

Revisiting Hansen Solubility Parameters by Including Thermodynamics.

Louwerse MJ, Maldonado A, Rousseau S, Moreau-Masselon C, Roux B, Rothenberg G.

Chemphyschem. 2017 Nov 3;18(21):2999-3006. doi: 10.1002/cphc.201700408. Epub 2017 Oct 6.

38.

Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids.

Li H, Chowdhary J, Huang L, He X, MacKerell AD Jr, Roux B.

J Chem Theory Comput. 2017 Sep 12;13(9):4535-4552. doi: 10.1021/acs.jctc.7b00262. Epub 2017 Aug 8.

39.

Establishing and testing a catchment water footprint framework to inform sustainable irrigation water use for an aquifer under stress.

le Roux B, van der Laan M, Vahrmeijer T, Bristow KL, Annandale JG.

Sci Total Environ. 2017 Dec 1;599-600:1119-1129. doi: 10.1016/j.scitotenv.2017.04.170. Epub 2017 May 12.

PMID:
28511357
40.

Ion channels and ion selectivity.

Roux B.

Essays Biochem. 2017 May 9;61(2):201-209. doi: 10.1042/EBC20160074. Print 2017 May 9. Review.

41.

Probing the Effects of Gating on the Ion Occupancy of the K+ Channel Selectivity Filter Using Two-Dimensional Infrared Spectroscopy.

Kratochvil HT, Maj M, Matulef K, Annen AW, Ostmeyer J, Perozo E, Roux B, Valiyaveetil FI, Zanni MT.

J Am Chem Soc. 2017 Jul 5;139(26):8837-8845. doi: 10.1021/jacs.7b01594. Epub 2017 May 12.

42.

Tyrosine Kinase Activation and Conformational Flexibility: Lessons from Src-Family Tyrosine Kinases.

Meng Y, Pond MP, Roux B.

Acc Chem Res. 2017 May 16;50(5):1193-1201. doi: 10.1021/acs.accounts.7b00012. Epub 2017 Apr 20.

PMID:
28426203
43.

Inversion of the Side-Chain Stereochemistry of Indvidual Thr or Ile Residues in a Protein Molecule: Impact on the Folding, Stability, and Structure of the ShK Toxin.

Dang B, Shen R, Kubota T, Mandal K, Bezanilla F, Roux B, Kent SB.

Angew Chem Int Ed Engl. 2017 Mar 13;56(12):3324-3328. doi: 10.1002/anie.201612398. Epub 2017 Feb 14.

44.

Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core.

Gates ZP, Baxa MC, Yu W, Riback JA, Li H, Roux B, Kent SB, Sosnick TR.

Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):2241-2246. doi: 10.1073/pnas.1609579114. Epub 2017 Feb 13.

45.

Molecular Structure of Canonical Liquid Crystal Interfaces.

Sadati M, Ramezani-Dakhel H, Bu W, Sevgen E, Liang Z, Erol C, Rahimi M, Taheri Qazvini N, Lin B, Abbott NL, Roux BT, Schlossman ML, de Pablo JJ.

J Am Chem Soc. 2017 Mar 15;139(10):3841-3850. doi: 10.1021/jacs.7b00167. Epub 2017 Mar 1.

PMID:
28177227
46.

Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies.

Simonson T, Hummer G, Roux B.

J Phys Chem A. 2017 Feb 23;121(7):1525-1530. doi: 10.1021/acs.jpca.6b12691. Epub 2017 Feb 13.

PMID:
28152306
47.

Conformational Transitions and Alternating-Access Mechanism in the Sarcoplasmic Reticulum Calcium Pump.

Das A, Rui H, Nakamoto R, Roux B.

J Mol Biol. 2017 Mar 10;429(5):647-666. doi: 10.1016/j.jmb.2017.01.007. Epub 2017 Jan 16.

48.

Understanding Atomic-Scale Behavior of Liquid Crystals at Aqueous Interfaces.

Ramezani-Dakhel H, Sadati M, Rahimi M, Ramirez-Hernandez A, Roux B, de Pablo JJ.

J Chem Theory Comput. 2017 Jan 10;13(1):237-244. doi: 10.1021/acs.jctc.6b00844. Epub 2016 Dec 12.

PMID:
27936703
49.

CHARMM-GUI 10 years for biomolecular modeling and simulation.

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 Jr, Klauda JB, Qi Y, Im W.

J Comput Chem. 2017 Jun 5;38(15):1114-1124. doi: 10.1002/jcc.24660. Epub 2016 Nov 14. Review.

50.

The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape.

Fajer M, Meng Y, Roux B.

J Phys Chem B. 2017 Apr 20;121(15):3352-3363. doi: 10.1021/acs.jpcb.6b08409. Epub 2016 Oct 28.

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