Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.
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Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structuresHigh-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulationsAssessing the Current State of Amber Force Field Modifications for DNABridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residueComputing Molecular Devices in L.major through Transcriptome Analysis: Structured Simulation ApproachConvergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structureStructural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamicsMolecular modeling of nucleic acid structure: energy and samplingStructural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry RoutesStacking in RNA: NMR of Four Tetramers Benchmark Molecular DynamicsComplete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations.Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations.Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry.Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptaseStructure and Dynamics of DNA and RNA Double Helices Obtained from the GGGGCC and CCCCGG Hexanucleotide Repeats That Are the Hallmark of C9FTD/ALS Diseases.Directional mechanical stability of Bacteriophage φ29 motor's 3WJ-pRNA: Extraordinary robustness along portal axisDisparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics.Computational study of unfolding and regulation mechanism of preQ1 riboswitches.Origin, diversification and substrate specificity in the family of NCS1/FUR transporters.Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model.Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study.NAFlex: a web server for the study of nucleic acid flexibility.Structural fidelity and NMR relaxation analysis in a prototype RNA hairpinComparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations.The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systemsKissing loop interaction in adenine riboswitch: insights from umbrella sampling simulationsStructural and functional consequences of phosphate-arsenate substitutions in selected nucleotides: DNA, RNA, and ATP.Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields.Selective Preference of Parallel DNA Triplexes Is Due to the Disruption of Hoogsteen Hydrogen Bonds Caused by the Severe Nonisostericity between the G*GC and T*AT Triplets.Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments.Current status of protein force fields for molecular dynamics simulations.Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform.
P2860
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P2860
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.
description
2011 nî lūn-bûn
@nan
2011年の論文
@ja
2011年論文
@yue
2011年論文
@zh-hant
2011年論文
@zh-hk
2011年論文
@zh-mo
2011年論文
@zh-tw
2011年论文
@wuu
2011年论文
@zh
2011年论文
@zh-cn
name
Refinement of the Cornell et a ...... f Glycosidic Torsion Profiles.
@en
type
label
Refinement of the Cornell et a ...... f Glycosidic Torsion Profiles.
@en
prefLabel
Refinement of the Cornell et a ...... f Glycosidic Torsion Profiles.
@en
P2093
P2860
P50
P356
P1476
Refinement of the Cornell et a ...... f Glycosidic Torsion Profiles.
@en
P2093
Arnošt Mládek
Jiří Sponer
Marie Zgarbová
Petr Jurečka
P2860
P304
P356
10.1021/CT200162X
P577
2011-08-02T00:00:00Z