Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures.
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MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and AllosteryIntegrating chemical footprinting data into RNA secondary structure predictionEnsemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknotEntropic stabilization of the folded states of RNA due to macromolecular crowdingLoop and stem dynamics during RNA hairpin folding and unfolding.Thermodynamics of RNA structures by Wang-Landau sampling.Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity.RNAiFOLD: a constraint programming algorithm for RNA inverse folding and molecular design.Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping.Absence of knots in known RNA structures.A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures.Free energy landscape and multiple folding pathways of an H-type RNA pseudoknot.Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulationsA magnesium-induced triplex pre-organizes the SAM-II riboswitch.Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme.RNA under tension: Folding Landscapes, Kinetic partitioning Mechanism, and Molecular TensegrityMimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel.Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulatorReduced model captures Mg(2+)-RNA interaction free energy of riboswitchesCooperative and directional folding of the preQ1 riboswitch aptamer domain.Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for -1 ribosomal frameshifting stimulation.Pseudoknots in RNA folding landscapes.How do metal ions direct ribozyme folding?Using simulations and kinetic network models to reveal the dynamics and functions of riboswitchesSalt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension.Theory for RNA folding, stretching, and melting including loops and salt.Kinetic mechanism of conformational switch between bistable RNA hairpins.Kinetic partitioning mechanism of HDV ribozyme folding.Folding kinetics for the conformational switch between alternative RNA structures.Physics-based de novo prediction of RNA 3D structures.Many-body effect in ion binding to RNA.Salt contribution to the flexibility of single-stranded nucleic acid offinite length.New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation.Nanopore electric snapshots of an RNA tertiary folding pathway.What Can Human-Guided Simulations Bring to RNA Folding?The thermodynamics and kinetics of a nucleotide base pair.Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.Development and Applications of Coarse-Grained Models for RNA
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Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures.
description
article científic
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article scientifique
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articolo scientifico
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artigo científico
@pt
bilimsel makale
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scientific article published on 05 October 2009
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vedecký článok
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vetenskaplig artikel
@sv
videnskabelig artikel
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vědecký článek
@cs
name
Assembly mechanisms of RNA pse ...... stituent secondary structures.
@en
Assembly mechanisms of RNA pse ...... stituent secondary structures.
@nl
type
label
Assembly mechanisms of RNA pse ...... stituent secondary structures.
@en
Assembly mechanisms of RNA pse ...... stituent secondary structures.
@nl
prefLabel
Assembly mechanisms of RNA pse ...... stituent secondary structures.
@en
Assembly mechanisms of RNA pse ...... stituent secondary structures.
@nl
P2093
P2860
P356
P1476
Assembly mechanisms of RNA pse ...... stituent secondary structures.
@en
P2093
D Thirumalai
David L Pincus
Samuel S Cho
P2860
P304
17349-17354
P356
10.1073/PNAS.0906625106
P407
P577
2009-10-05T00:00:00Z