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Items: 1 to 50 of 547

1.

Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual Topology Free Energy Perturbation Approach in NAMD.

Jiang W, Chipot C, Roux B.

J Chem Inf Model. 2019 Aug 14. doi: 10.1021/acs.jcim.9b00362. [Epub ahead of print]

PMID:
31411473
2.

Stomatal aperture and turnover of ABA receptors are regulated by Arabidopsis ALIX.

García-León M, Cuyas L, Abd El-Moneim D, Rodriguez L, Belda-Palazon B, Sánchez-Quant E, Fernández Y, Roux B, Zamarreño AM, Garcia-Mina JM, Nussaume L, Rodriguez PL, Paz-Ares J, Leonhardt N, Rubio V.

Plant Cell. 2019 Jul 30. pii: tpc.00399.2019. doi: 10.1105/tpc.19.00399. [Epub ahead of print]

PMID:
31363038
3.

CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations.

Qi Y, Lee J, Cheng X, Shen R, Islam SM, Roux B, Im W.

J Comput Chem. 2019 Jul 22. doi: 10.1002/jcc.26032. [Epub ahead of print]

PMID:
31329318
4.

Identification of nitrite treated tuna fish meat via the determination of nitrous oxide by head space-gas chromatography/mass spectrometry.

Niederer M, Lang S, Roux B, Stebler T, Hohl C.

F1000Res. 2019 May 22;8:711. doi: 10.12688/f1000research.19304.1. eCollection 2019.

5.

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.

Bedrov D, Piquemal JP, Borodin O, MacKerell AD Jr, Roux B, Schröder C.

Chem Rev. 2019 Jul 10;119(13):7940-7995. doi: 10.1021/acs.chemrev.8b00763. Epub 2019 May 29.

PMID:
31141351
6.

Perfusion Bioreactor Culture of Bone Marrow Stromal Cells Enhances Cranial Defect Regeneration.

Gandhi JK, Kao SW, Roux BM, Rodriguez RA, Tang SJ, Fisher JP, Cheng MH, Brey EM.

Plast Reconstr Surg. 2019 May;143(5):993e-1002e. doi: 10.1097/PRS.0000000000005529.

PMID:
31033820
7.

Long intergenic non-coding RNAs regulate human lung fibroblast function: Implications for idiopathic pulmonary fibrosis.

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

Sci Rep. 2019 Apr 15;9(1):6020. doi: 10.1038/s41598-019-42292-w.

8.

Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase.

Ellis-Guardiola K, Rui H, Beckner RL, Srivastava P, Sukumar N, Roux B, Lewis JC.

Biochemistry. 2019 Mar 26;58(12):1616-1626. doi: 10.1021/acs.biochem.9b00031. Epub 2019 Mar 5.

PMID:
30786206
9.

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.

10.

[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
11.

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.

12.

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 17;123(2):629. doi: 10.1021/acs.jpca.8b12337. Epub 2019 Jan 2. No abstract available.

13.

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
14.

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. 2019 Mar;178(3):331-340. doi: 10.1007/s00431-018-3300-1. Epub 2018 Dec 1.

PMID:
30506396
15.

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 Dec 11;14(12):6748-6749. doi: 10.1021/acs.jctc.8b01075. Epub 2018 Nov 27. No abstract available.

PMID:
30480445
16.

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
17.

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
18.

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
19.

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. 2019 Apr;13(1):71-74. doi: 10.1007/s12104-018-9854-z. Epub 2018 Oct 4.

PMID:
30284668
20.

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.

21.

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
22.

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
23.

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.

24.

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
25.

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
26.

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. Erratum in: J Phys Chem A. 2019 Jan 17;123(2):629.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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
34.

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.

35.

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.

36.

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. Erratum in: J Chem Theory Comput. 2018 Dec 11;14(12):6748-6749.

37.

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.

38.

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
39.

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.

40.

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.

41.

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
42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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
48.

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.

49.

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.

50.

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.

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