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Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations.

Journal of chemical theory and computation

Lev B, Roux B, Noskov SY.
PMID: 26592407
J Chem Theory Comput. 2013 Sep 10;9(9):4165-75. doi: 10.1021/ct400296w. Epub 2013 Aug 26.

Methods directly evaluating the hydration structure and thermodynamics of physiologically relevant cations (Na(+), K(+), Cl(-), etc.) have wide ranging applications in the fields of inorganic, physical, and biological chemistry. All-atom simulations based on accurate potential energy surfaces appear to...

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Lev B, Roux B, Noskov SY. Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations. J Chem Theory Comput. 2013;9(9):4165-75doi: 10.1021/ct400296w.
Lev, B., Roux, B., & Noskov, S. Y. (2013). Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations. Journal of chemical theory and computation, 9(9), 4165-75. https://doi.org/10.1021/ct400296w
Lev, Bogdan, et al. "Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations." Journal of chemical theory and computation vol. 9,9 (2013): 4165-75. doi: https://doi.org/10.1021/ct400296w
Lev B, Roux B, Noskov SY. Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations. J Chem Theory Comput. 2013 Sep 10;9(9):4165-75. doi: 10.1021/ct400296w. Epub 2013 Aug 26. PMID: 26592407.
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Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model.

The journal of physical chemistry letters

Huang J, Lopes PE, Roux B, MacKerell AD.
PMID: 25247054
J Phys Chem Lett. 2014 Sep 18;5(18):3144-3150. doi: 10.1021/jz501315h. Epub 2014 Aug 27.

In this Perspective, we summarize recent efforts to include the explicit treatment of induced electronic polarization in biomolecular force fields. Methods used to treat polarizability, including the induced dipole, fluctuating charge, and classical Drude oscillator models, are presented, including...

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Huang J, Lopes PE, Roux B, et al. Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model. J Phys Chem Lett. 2014;5(18):3144-3150doi: 10.1021/jz501315h.
Huang, J., Lopes, P. E., Roux, B., & MacKerell, A. D. (2014). 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(18), 3144-3150. https://doi.org/10.1021/jz501315h
Huang, Jing, et al. "Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model." The journal of physical chemistry letters vol. 5,18 (2014): 3144-3150. doi: https://doi.org/10.1021/jz501315h
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. J Phys Chem Lett. 2014 Sep 18;5(18):3144-3150. doi: 10.1021/jz501315h. Epub 2014 Aug 27. PMID: 25247054; PMCID: PMC4167036.
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Antipodal focusing of seismic waves observed with the USArray.

Geophysical journal international

Retailleau L, Shapiro NM, Guilbert J, Campillo M, Roux P.
PMID: 26074723
Geophys J Int. 2014 Sep 10;199(2):1030-1042. doi: 10.1093/gji/ggu309. eCollection 2014 Nov 01.

We present an analysis of the

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Retailleau L, Shapiro NM, Guilbert J, et al. Antipodal focusing of seismic waves observed with the USArray. Geophys J Int. 2014;199(2):1030-1042doi: 10.1093/gji/ggu309.
Retailleau, L., Shapiro, N. M., Guilbert, J., Campillo, M., & Roux, P. (2014). Antipodal focusing of seismic waves observed with the USArray. Geophysical journal international, 199(2), 1030-1042. https://doi.org/10.1093/gji/ggu309
Retailleau, L, et al. "Antipodal focusing of seismic waves observed with the USArray." Geophysical journal international vol. 199,2 (2014): 1030-1042. doi: https://doi.org/10.1093/gji/ggu309
Retailleau L, Shapiro NM, Guilbert J, Campillo M, Roux P. Antipodal focusing of seismic waves observed with the USArray. Geophys J Int. 2014 Sep 10;199(2):1030-1042. doi: 10.1093/gji/ggu309. eCollection 2014 Nov 01. PMID: 26074723; PMCID: PMC4461126.
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Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer.

Journal of chemical theory and computation

Jiang W, Luo Y, Maragliano L, Roux B.
PMID: 26605623
J Chem Theory Comput. 2012 Nov 13;8(11):4672-80. doi: 10.1021/ct300468g. Epub 2012 Oct 17.

An extremely scalable computational strategy is described for calculations of the potential of mean force (PMF) in multidimensions on massively distributed supercomputers. The approach involves coupling thousands of umbrella sampling (US) simulation windows distributed to cover the space of...

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Jiang W, Luo Y, Maragliano L, et al. Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer. J Chem Theory Comput. 2012;8(11):4672-80doi: 10.1021/ct300468g.
Jiang, W., Luo, Y., Maragliano, L., & Roux, B. (2012). Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer. Journal of chemical theory and computation, 8(11), 4672-80. https://doi.org/10.1021/ct300468g
Jiang, Wei, et al. "Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer." Journal of chemical theory and computation vol. 8,11 (2012): 4672-80. doi: https://doi.org/10.1021/ct300468g
Jiang W, Luo Y, Maragliano L, Roux B. Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer. J Chem Theory Comput. 2012 Nov 13;8(11):4672-80. doi: 10.1021/ct300468g. Epub 2012 Oct 17. PMID: 26605623.
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A chimeric transcript containing a 16 S rRNA and a potential mRNA in chloroplasts of Euglena gracilis.

Plant molecular biology

Koller B, Roux E, Montandon PE, Stutz E.
PMID: 24277565
Plant Mol Biol. 1988 Jul;10(4):339-47. doi: 10.1007/BF00029884.

The chloroplast genome of Euglena gracilis contains a supplementary gene for a 16 S rRNA (s16 S rrn gene), which is not part of a complete rrn operon. An open reading frame (ORF406) is located downstream of the s16...

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Koller B, Roux E, Montandon PE, et al. A chimeric transcript containing a 16 S rRNA and a potential mRNA in chloroplasts of Euglena gracilis. Plant Mol Biol. 1988;10(4):339-47doi: 10.1007/BF00029884.
Koller, B., Roux, E., Montandon, P. E., & Stutz, E. (1988). A chimeric transcript containing a 16 S rRNA and a potential mRNA in chloroplasts of Euglena gracilis. Plant molecular biology, 10(4), 339-47. https://doi.org/10.1007/BF00029884
Koller, B, et al. "A chimeric transcript containing a 16 S rRNA and a potential mRNA in chloroplasts of Euglena gracilis." Plant molecular biology vol. 10,4 (1988): 339-47. doi: https://doi.org/10.1007/BF00029884
Koller B, Roux E, Montandon PE, Stutz E. A chimeric transcript containing a 16 S rRNA and a potential mRNA in chloroplasts of Euglena gracilis. Plant Mol Biol. 1988 Jul;10(4):339-47. doi: 10.1007/BF00029884. PMID: 24277565.
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AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON .

Journal of chemical theory and computation

Huang L, Roux B.
PMID: 24223528
J Chem Theory Comput. 2013 Aug 13;9(8). doi: 10.1021/ct4003477.

Classical molecular dynamics (MD) simulations based on atomistic models are increasingly used to study a wide range of biological systems. A prerequisite for meaningful results from such simulations is an accurate molecular mechanical force field. Most biomolecular simulations are...

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Huang L, Roux B. AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON . J Chem Theory Comput. 2013;9(8)doi: 10.1021/ct4003477.
Huang, L., & Roux, B. (2013). AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON . Journal of chemical theory and computation, 9(8), . https://doi.org/10.1021/ct4003477
Huang, Lei, and Roux, Benoît. "AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON ." Journal of chemical theory and computation vol. 9,8 (2013). doi: https://doi.org/10.1021/ct4003477
Huang L, Roux B. AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON . J Chem Theory Comput. 2013 Aug 13;9(8). doi: 10.1021/ct4003477. PMID: 24223528; PMCID: PMC3819940.
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Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD.

Computer physics communications

Jiang W, Phillips JC, Huang L, Fajer M, Meng Y, Gumbart JC, Luo Y, Schulten K, Roux B.
PMID: 24944348
Comput Phys Commun. 2014 Mar;185(3):908-916. doi: 10.1016/j.cpc.2013.12.014.

Computational methodologies that couple the dynamical evolution of a set of replicated copies of a system of interest offer powerful and flexible approaches to characterize complex molecular processes. Such multiple copy algorithms (MCAs) can be used to enhance sampling,...

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Jiang W, Phillips JC, Huang L, et al. Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD. Comput Phys Commun. 2014;185(3):908-916doi: 10.1016/j.cpc.2013.12.014.
Jiang, W., Phillips, J. C., Huang, L., Fajer, M., Meng, Y., Gumbart, J. C., Luo, Y., Schulten, K., & Roux, B. (2014). Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD. Computer physics communications, 185(3), 908-916. https://doi.org/10.1016/j.cpc.2013.12.014
Jiang, Wei, et al. "Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD." Computer physics communications vol. 185,3 (2014): 908-916. doi: https://doi.org/10.1016/j.cpc.2013.12.014
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. Comput Phys Commun. 2014 Mar;185(3):908-916. doi: 10.1016/j.cpc.2013.12.014. PMID: 24944348; PMCID: PMC4059768.
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Corrigendum: Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress.

Scientific reports

Zorrilla-Fontanesi Y, Rouard M, Cenci A, Kissel E, Do H, Dubois E, Nidelet S, Roux N, Swennen R, Carpentier SC.
PMID: 27203802
Sci Rep. 2016 May 20;7:25683. doi: 10.1038/srep25683.

No abstract available.

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Zorrilla-Fontanesi Y, Rouard M, Cenci A, et al. Corrigendum: Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress. Sci Rep. 2016;7:25683doi: 10.1038/srep25683.
Zorrilla-Fontanesi, Y., Rouard, M., Cenci, A., Kissel, E., Do, H., Dubois, E., Nidelet, S., Roux, N., Swennen, R., & Carpentier, S. C. (2016). Corrigendum: Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress. Scientific reports, 725683. https://doi.org/10.1038/srep25683
Zorrilla-Fontanesi, Yasmín, et al. "Corrigendum: Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress." Scientific reports vol. 7 (2016): 25683. doi: https://doi.org/10.1038/srep25683
Zorrilla-Fontanesi Y, Rouard M, Cenci A, Kissel E, Do H, Dubois E, Nidelet S, Roux N, Swennen R, Carpentier SC. Corrigendum: Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress. Sci Rep. 2016 May 20;7:25683. doi: 10.1038/srep25683. PMID: 27203802; PMCID: PMC4874233.
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The application of portable microchip electrophoresis for the screening and comparative analysis of synthetic cathinone seizures.

Forensic science international

Lloyd A, Russell M, Blanes L, Somerville R, Doble P, Roux C, Kumar CG.
PMID: 25016536
Forensic Sci Int. 2014 Sep;242:16-23. doi: 10.1016/j.forsciint.2014.06.013. Epub 2014 Jun 24.

Variation in the chemical composition of illicit tablets and powders is common among samples within a given drug seizure. Using microchip electrophoresis (ME), multiple tablets can be screened in a cost-effective and timely manner. This method could be used...

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Lloyd A, Russell M, Blanes L, et al. The application of portable microchip electrophoresis for the screening and comparative analysis of synthetic cathinone seizures. Forensic Sci Int. 2014;242:16-23doi: 10.1016/j.forsciint.2014.06.013.
Lloyd, A., Russell, M., Blanes, L., Somerville, R., Doble, P., Roux, C., & Kumar, C. G. (2014). The application of portable microchip electrophoresis for the screening and comparative analysis of synthetic cathinone seizures. Forensic science international, 24216-23. https://doi.org/10.1016/j.forsciint.2014.06.013
Lloyd, Aimee, et al. "The application of portable microchip electrophoresis for the screening and comparative analysis of synthetic cathinone seizures." Forensic science international vol. 242 (2014): 16-23. doi: https://doi.org/10.1016/j.forsciint.2014.06.013
Lloyd A, Russell M, Blanes L, Somerville R, Doble P, Roux C, Kumar CG. The application of portable microchip electrophoresis for the screening and comparative analysis of synthetic cathinone seizures. Forensic Sci Int. 2014 Sep;242:16-23. doi: 10.1016/j.forsciint.2014.06.013. Epub 2014 Jun 24. PMID: 25016536.
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Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model.

Journal of chemical theory and computation

Shivakumar D, Deng Y, Roux B.
PMID: 26609601
J Chem Theory Comput. 2009 Apr 14;5(4):919-30. doi: 10.1021/ct800445x. Epub 2009 Mar 24.

Accurate determination of absolute solvation free energy plays a critical role in numerous areas of biomolecular modeling and drug discovery. A quantitative representation of ligand and receptor desolvation, in particular, is an essential component of current docking and scoring...

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Shivakumar D, Deng Y, Roux B. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model. J Chem Theory Comput. 2009;5(4):919-30doi: 10.1021/ct800445x.
Shivakumar, D., Deng, Y., & Roux, B. (2009). Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model. Journal of chemical theory and computation, 5(4), 919-30. https://doi.org/10.1021/ct800445x
Shivakumar, Devleena, et al. "Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model." Journal of chemical theory and computation vol. 5,4 (2009): 919-30. doi: https://doi.org/10.1021/ct800445x
Shivakumar D, Deng Y, Roux B. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model. J Chem Theory Comput. 2009 Apr 14;5(4):919-30. doi: 10.1021/ct800445x. Epub 2009 Mar 24. PMID: 26609601.
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Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator.

Journal of chemical theory and computation

Anisimov VM, Lamoureux G, Vorobyov IV, Huang N, Roux B, MacKerell AD.
PMID: 26641126
J Chem Theory Comput. 2005 Jan;1(1):153-68. doi: 10.1021/ct049930p.

A procedure to determine the electrostatic parameters has been developed for a polarizable empirical force field based on the classical Drude oscillator model. Atomic charges and polarizabilities for a given molecule of interest were derived from restrained fitting to...

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Anisimov VM, Lamoureux G, Vorobyov IV, et al. Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. J Chem Theory Comput. 2005;1(1):153-68doi: 10.1021/ct049930p.
Anisimov, V. M., Lamoureux, G., Vorobyov, I. V., Huang, N., Roux, B., & MacKerell, A. D. (2005). Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. Journal of chemical theory and computation, 1(1), 153-68. https://doi.org/10.1021/ct049930p
Anisimov, Victor M, et al. "Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator." Journal of chemical theory and computation vol. 1,1 (2005): 153-68. doi: https://doi.org/10.1021/ct049930p
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. J Chem Theory Comput. 2005 Jan;1(1):153-68. doi: 10.1021/ct049930p. PMID: 26641126.
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PARTICIPATION OF EXTRACELLULAR NUCLEOTIDES IN THE WOUND RESPONSE OF DASYCLADUS VERMICULARIS AND ACETABULARIA ACETABULUM (DASYCLADALES, CHLOROPHYTA)(1).

Journal of phycology

Torres J, Rivera A, Clark G, Roux SJ.
PMID: 27039864
J Phycol. 2008 Dec;44(6):1504-11. doi: 10.1111/j.1529-8817.2008.00602.x.

As assayed by fluorescent reporter dyes, nitric oxide (NO) and H2 O2 , two downstream signaling agents induced by wounding in the alga Dasycladus vermicularis (Scop.) Krasser, can also be induced in unwounded Dasycladus cells by μM Adenosine 5'[γ-thio]triphosphate...

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Torres J, Rivera A, Clark G, et al. PARTICIPATION OF EXTRACELLULAR NUCLEOTIDES IN THE WOUND RESPONSE OF DASYCLADUS VERMICULARIS AND ACETABULARIA ACETABULUM (DASYCLADALES, CHLOROPHYTA)(1). J Phycol. 2008;44(6):1504-11doi: 10.1111/j.1529-8817.2008.00602.x.
Torres, J., Rivera, A., Clark, G., & Roux, S. J. (2008). PARTICIPATION OF EXTRACELLULAR NUCLEOTIDES IN THE WOUND RESPONSE OF DASYCLADUS VERMICULARIS AND ACETABULARIA ACETABULUM (DASYCLADALES, CHLOROPHYTA)(1). Journal of phycology, 44(6), 1504-11. https://doi.org/10.1111/j.1529-8817.2008.00602.x
Torres, Jonathan, et al. "PARTICIPATION OF EXTRACELLULAR NUCLEOTIDES IN THE WOUND RESPONSE OF DASYCLADUS VERMICULARIS AND ACETABULARIA ACETABULUM (DASYCLADALES, CHLOROPHYTA)(1)." Journal of phycology vol. 44,6 (2008): 1504-11. doi: https://doi.org/10.1111/j.1529-8817.2008.00602.x
Torres J, Rivera A, Clark G, Roux SJ. PARTICIPATION OF EXTRACELLULAR NUCLEOTIDES IN THE WOUND RESPONSE OF DASYCLADUS VERMICULARIS AND ACETABULARIA ACETABULUM (DASYCLADALES, CHLOROPHYTA)(1). J Phycol. 2008 Dec;44(6):1504-11. doi: 10.1111/j.1529-8817.2008.00602.x. PMID: 27039864.
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Showing 13 to 24 of 1157 entries