Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments

Zhengyue Zhang; Jennifer Vögele; Klaudia Mráziková; Holger Kruse; Xiaohui Cang; Jens Wöhnert; Miroslav Krepl; Jiří Šponer

doi:10.1021/acs.jpcb.0c10192

Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.0c10192 ◽

2021 ◽

Vol 125 (3) ◽

pp. 825-840

Author(s):

Zhengyue Zhang ◽

Jennifer Vögele ◽

Klaudia Mráziková ◽

Holger Kruse ◽

Xiaohui Cang ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Rna Structure ◽

Dynamics Simulations

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RNA structure refinement and force field evaluation using molecular dynamics simulations

Proceedings of the 2011 TeraGrid Conference on Extreme Digital Discovery - TG '11 ◽

10.1145/2016741.2016745 ◽

2011 ◽

Author(s):

Niel Henriksen ◽

Thomas E. Cheatham

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Rna Structure ◽

Structure Refinement ◽

Field Evaluation ◽

Dynamics Simulations

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Structure of phosphorus-selenium glasses: results from ab initio molecular dynamics simulations

Molecular Physics ◽

10.1080/002689700162045 ◽

2000 ◽

Vol 98 (11) ◽

pp. 701-707

Author(s):

Alessandro Sergi, Mauro Ferrario, Francesco Bu

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Ab Initio Molecular Dynamics ◽

Dynamics Simulations

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Tracer diffusion in perfectly aligned liquid crystalline phases Kinetic theory and molecular dynamics simulations

Molecular Physics ◽

10.1080/00268979709482789 ◽

1997 ◽

Vol 91 (6) ◽

pp. 993-1003 ◽

Cited By ~ 1

Author(s):

ANJALI KHARE ◽

DAVID KOFKE ◽

GLENN EVANS

Keyword(s):

Molecular Dynamics ◽

Kinetic Theory ◽

Molecular Dynamics Simulations ◽

Liquid Crystalline ◽

Tracer Diffusion ◽

Crystalline Phases ◽

Liquid Crystalline Phases ◽

Dynamics Simulations

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ERRATUM Molecular dynamics simulations of liquid crystal phases using atomistic potentials

Molecular Physics ◽

10.1080/002689798167430 ◽

1998 ◽

Vol 95 (1) ◽

pp. 121-121

Author(s):

CARL MCBRIDE MARK R. WILSON JUDITH A. K.

Keyword(s):

Molecular Dynamics ◽

Liquid Crystal ◽

Molecular Dynamics Simulations ◽

Crystal Phases ◽

Dynamics Simulations ◽

Liquid Crystal Phases

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Nonequilibrium Molecular Dynamics Simulations of 3-Methylhexane: The Effect of Inter- and Intramolecular Potential Models on Simulated Viscosity

The Journal of Physical Chemistry A ◽

10.1021/jp971476g ◽

1997 ◽

Vol 101 (27) ◽

pp. 5026-5026

Author(s):

Maija Lahtela ◽

Tapani A. Pakkanen ◽

Richard L. Rowley

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Nonequilibrium Molecular Dynamics ◽

Potential Models ◽

Dynamics Simulations

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Assessment of all-atom potentials for modeling membranes: molecular dynamics simulations of solid and liquid alkanes and crystals of phospholipid fragments

Journal de Chimie Physique ◽

10.1051/jcp/1997941482 ◽

1997 ◽

Vol 94 ◽

pp. 1482-1502 ◽

Cited By ~ 27

Author(s):

DJ Tobias ◽

K Tu ◽

ML Klein

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations ◽

Liquid Alkanes

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Molecular Dynamics Simulations of Retrograde Condensation in Nanoporous Shale

Proceedings of the 3rd Unconventional Resources Technology Conference ◽

10.15530/urtec-2015-2172738 ◽

2015 ◽

Cited By ~ 1

Author(s):

William R. Welch ◽

Mohammad Piri

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Retrograde Condensation ◽

Dynamics Simulations

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MOLECULAR DYNAMICS SIMULATIONS OF RAYLEIGH AND FIRST WIND-INDUCED BREAKUP

Atomization and Sprays ◽

10.1615/atomizspr.2011002906 ◽

2011 ◽

Vol 21 (4) ◽

pp. 275-281 ◽

Cited By ~ 4

Author(s):

Kurt F. Ludwig ◽

Michael Micci

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations

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MOLECULAR DYNAMICS SIMULATIONS OF ATOMIZATION AND SPRAY PHENOMENA

Atomization and Sprays ◽

10.1615/atomizspr.v11.i4.40 ◽

2001 ◽

Vol 11 (4) ◽

pp. 351-363 ◽

Cited By ~ 7

Author(s):

Teresa L. Kaltz ◽

Lyle N. Long

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations

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Molecular Dynamics Simulations of Glutamate Diffusion in Synaptic Cleft

Critical Reviews in Neurobiology ◽

10.1615/critrevneurobiol.v18.i1-2.70 ◽

2006 ◽

Vol 18 (1-2) ◽

pp. 61-69 ◽

Cited By ~ 4

Author(s):

Sean M. Cory ◽

Mladen I. Glavinovic

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Synaptic Cleft ◽

Dynamics Simulations

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