Molecular dynamics simulations of RNA: an in silico single molecule approach. - Test2 - elhamkhani - TriplyDB

Molecular dynamics simulations of RNA: an in silico single molecule approach.

Molecular dynamics simulations of RNA: an in silico single molecule approach.

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Single molecule fluorescence approaches shed light on intracellular RNAs Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA The Conformational Landscape of the Ribosomal Protein S15 and Its Influence on the Protein Interaction with 16S RNA Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure RNA and protein 3D structure modeling: similarities and differences.iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge Molecular dynamics study of the ribosomal A-site.A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm Mechanism of action of cyclophilin a explored by metadynamics simulations.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 Pairs Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site.The purine riboswitch as a model system for exploring RNA biology and chemistry Toward a consensus view of duplex RNA flexibility Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome.Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics.Multiscale methods for computational RNA enzymology.Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis.Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site.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.A novel implicit solvent model for simulating the molecular dynamics of RNA Dynamics of tRNA at different levels of hydration.Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.Elbow flexibility of the kt38 RNA kink-turn motif investigated by free-energy molecular dynamics simulations.Computational approaches to predicting the impact of novel bases on RNA structure and stability.Free energy calculation of modified base-pair formation in explicit solvent: A predictive model.Binding of the bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular dynamics simulations.Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide.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.Effects of hypoxanthine substitution in peptide nucleic acids targeting KRAS2 oncogenic mRNA molecules: theory and experiment.Classical electrostatics for biomolecular simulations.Nucleic acid catalysis: metals, nucleobases, and other cofactors.Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs.Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations

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Molecular dynamics simulations of RNA: an in silico single molecule approach.

http://www.wikidata.org/entity/Q36058510

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2007 nî lūn-bûn

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Molecular dynamics simulations of RNA: an in silico single molecule approach.

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Molecular dynamics simulations of RNA: an in silico single molecule approach.

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Molecular dynamics simulations of RNA: an in silico single molecule approach

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Nad'a Spacková

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S Elizabeth McDowell

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P2860

An RNA gene expressed during cortical development evolved rapidly in humans

Single-Stranded Adenine-Rich DNA and RNA Retain Structural Characteristics of Their Respective Double-Stranded Conformations and Show Directional Differences in Stacking Pattern †

The Protein Data Bank

Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif

Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference

Molecular dynamics simulations of sarcin-ricin rRNA motif.

Structural and evolutionary classification of G/U wobble basepairs in the ribosome

The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA

Hfq variant with altered RNA binding functions

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169-184

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scholarly article

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10.1002/BIP.20620

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2

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85

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17080418

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2018183

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