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Molecular dynamics simulations of sarcin-ricin rRNA motif.Structural and evolutionary classification of G/U wobble basepairs in the ribosomeTwo 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG)How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid:ribonucleic acid duplexMolecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine.Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformersConformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale.Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer.Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets.Theoretical calculation of the NMR spin-spin coupling constants and the NMR shifts allow distinguishability between the specific direct and the water-mediated binding of a divalent metal cation to guanine.Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective.Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex.Theoretical study of the scalar coupling constants across the noncovalent contacts in RNA base pairs: the cis- and trans-watson-crick/sugar edge base pair family.Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.Structural interpretation of J coupling constants in guanosine and deoxyguanosine: modeling the effects of sugar pucker, backbone conformation, and base pairing.Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptaseA systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base PairsDynamics 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.Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts.Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates.Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations.Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosomeHinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired basesμABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNAThe role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozymeA G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancerElastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNAMolecular dynamics simulations of RNA: an in silico single molecule approach.Extended molecular dynamics of a c-kit promoter quadruplex.Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics.Molecular dynamics simulations and their application to four-stranded DNA.Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.Nature and magnitude of aromatic stacking of nucleic acid bases.Elbow flexibility of the kt38 RNA kink-turn motif investigated by free-energy molecular dynamics simulations.Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations.Selectivity of major isoquinoline alkaloids from Chelidonium majus towards telomeric G-quadruplex: A study using a transition-FRET (t-FRET) assay.
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P50
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researcher
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wetenschapper
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հետազոտող
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Jirí Sponer
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Jirí Sponer
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Jirí Sponer
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Jirí Sponer
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Jirí Sponer
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Jirí Sponer
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Jirí Sponer
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Jirí Sponer
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Jirí Sponer
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Jirí Sponer
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Jirí Sponer
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Jirí Sponer
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Jirí Sponer
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Jirí Sponer
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Jirí Sponer
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P106
P1153
7005068993
P31
P496
0000-0001-6558-6186