Dependence of A-RNA simulations on the choice of the force field and salt strength
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Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structuresMolecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structureQuantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?Computational exploration of mobile ion distributions around RNA duplexSubstrate recognition and specificity of double-stranded RNA binding proteins.Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site.Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosomeIon distributions around left- and right-handed DNA and RNA duplexes: a comparative study.Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexesReference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.Molecular Mechanism of Processive 3' to 5' RNA Translocation in the Active Subunit of the RNA Exosome Complex.Interconversion between parallel and antiparallel conformations of a 4H RNA junction in domain 3 of foot-and-mouth disease virus IRES captured by dynamics simulations.Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA.Genetic algorithms coupled with quantum mechanics for refinement of force fields for RNA simulation: a case study of glycosidic torsions in the canonical ribonucleosides.Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.All-atom crystal simulations of DNA and RNA duplexes.Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study.Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.Structure and mechanical properties of the ribosomal L1 stalk three-way junction.RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Evaluating nonpolarizable nucleic acid force fields: a systematic comparison of the nucleobases hydration free energies and chloroform-to-water partition coefficients.
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P2860
Dependence of A-RNA simulations on the choice of the force field and salt strength
description
im Januar 2009 veröffentlichter wissenschaftlicher Artikel
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wetenschappelijk artikel
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наукова стаття, опублікована у 2009
@uk
name
Dependence of A-RNA simulations on the choice of the force field and salt strength
@en
Dependence of A-RNA simulations on the choice of the force field and salt strength
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type
label
Dependence of A-RNA simulations on the choice of the force field and salt strength
@en
Dependence of A-RNA simulations on the choice of the force field and salt strength
@nl
prefLabel
Dependence of A-RNA simulations on the choice of the force field and salt strength
@en
Dependence of A-RNA simulations on the choice of the force field and salt strength
@nl
P2860
P356
P1476
Dependence of A-RNA simulations on the choice of the force field and salt strength
@en
P2093
Ivana Beššeová
Kamila Réblová
P2860
P356
10.1039/B911169G
P407
P577
2009-01-01T00:00:00Z