Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields.
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Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structuresConvergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)MoD-QM/MM Structural Refinement Method: Characterization of Hydrogen Bonding in the Oxytricha nova G-QuadruplexConformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale.A comparison of four different conformations adopted by human telomeric G-Quadruplex using Computer Simulations.Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EMExploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.Structural dynamics of human telomeric G-quadruplex loops studied by molecular dynamics simulations.Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexesImproved Generalized Born Solvent Model Parameters for Protein Simulations.Molecular dynamics and principal components of potassium binding with human telomeric intra-molecular G-quadruplex.Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.Extended molecular dynamics of a c-kit promoter quadruplex.Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.Parmbsc1: a refined force field for DNA simulations.Understanding the kinetic mechanism of RNA single base pair formationHairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations.The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.Computational docking simulations of a DNA-aptamer for argininamide and related ligands.Multiple stepwise pattern for potential of mean force in unfolding the thrombin binding aptamer in complex with Sr2+.Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.Complexes of the antitumoral drugs Doxorubicin and Sabarubicin with telomeric G-quadruplex in basket conformation: ground and excited state properties.Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis.Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.A single nucleotide resolution model for large-scale simulations of double stranded DNA.Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions.Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations.Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations.Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field ParametersThe critical effect of polarization on the dynamical structure of guanine quadruplex DNA.Insilico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level.RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands.Binding modes and pathway of RHPS4 to human telomeric G-quadruplex and duplex DNA probed by all-atom molecular dynamics simulations with explicit solvent.Conformational and electronic effects on the formation of anti cyclobutane pyrimidine dimers in G-quadruplex structures.Dynamics of fluorescent dyes attached to G-quadruplex DNA and their effect on FRET experiments.New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions.
P2860
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P2860
Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields.
description
2009 nî lūn-bûn
@nan
2009年の論文
@ja
2009年学术文章
@wuu
2009年学术文章
@zh-cn
2009年学术文章
@zh-hans
2009年学术文章
@zh-my
2009年学术文章
@zh-sg
2009年學術文章
@yue
2009年學術文章
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2009年學術文章
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name
Single Stranded Loops of Quadr ...... ng Nucleic Acids Force Fields.
@en
Single Stranded Loops of Quadr ...... ng Nucleic Acids Force Fields.
@nl
type
label
Single Stranded Loops of Quadr ...... ng Nucleic Acids Force Fields.
@en
Single Stranded Loops of Quadr ...... ng Nucleic Acids Force Fields.
@nl
prefLabel
Single Stranded Loops of Quadr ...... ng Nucleic Acids Force Fields.
@en
Single Stranded Loops of Quadr ...... ng Nucleic Acids Force Fields.
@nl
P2093
P50
P356
P1476
Single Stranded Loops of Quadr ...... ng Nucleic Acids Force Fields.
@en
P2093
Eva Fadrná
Joanna Sarzyñska
Modesto Orozco
Nad'a Špačková
Tadeusz Kulinski
P304
P356
10.1021/CT900200K
P577
2009-08-19T00:00:00Z