Prediction of the RNA Tertiary Structure Based on a Random Sampling Strategy and Parallel Mechanism [PDF]
Frontiers in Genetics, 2022 Background: Macromolecule structure prediction remains a fundamental challenge of bioinformatics. Over the past several decades, the Rosetta framework has provided solutions to diverse challenges in computational biology.
Zhendong Liu +5 more
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NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation [PDF]
Nature CommunicationsRNA plays a crucial role not only in information transfer as messenger RNA during gene expression but also in various biological functions as non-coding RNAs.
Yuki Kagaya +6 more
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RNA tertiary structure analysis by 2'-hydroxyl molecular interference [PDF]
Biochemistry, 2014 We introduce a melded chemical and computational approach for probing and modeling higher-order intramolecular tertiary interactions in RNA. 2'-Hydroxyl molecular interference (HMX) identifies nucleotides in highly packed regions of an RNA by exploiting ...
P. Homan +5 more
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Stabilization of RNA tertiary structure by monovalent cations.
Journal of Molecular Biology, 2000 The effects of monovalent cations (Li(+), Na(+), K(+), Rb(+), Cs(+), and NH4(+)) on the thermal stability of RNA tertiary structure were investigated by UV melting.
Ross Shiman, David E. Draper
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RNA tertiary structure and conformational dynamics revealed by BASH MaP [PDF]
eLifeThe functional effects of an RNA can arise from complex three-dimensional folds known as tertiary structures. However, predicting the tertiary structure of an RNA and whether an RNA adopts distinct tertiary conformations remains challenging.
Maxim Oleynikov, Samie R Jaffrey
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On the significance of an RNA tertiary structure prediction. [PDF]
RNA, 2010 Tertiary structure prediction is important for understanding structure–function relationships for RNAs whose structures are unknown and for characterizing RNA states recalcitrant to direct analysis. However, it is unknown what root-mean-square deviation (RMSD) corresponds to a statistically significant RNA tertiary structure prediction. We use discrete
Christine E. Hajdin +3 more
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Protonation of Trimethylamine N-Oxide (TMAO) is required for stabilization of RNA tertiary structure [PDF]
Biophysical Chemistry, 2013 The osmolyte trimethylamine N-oxide (TMAO) stabilizes the tertiary but not the secondary structures of RNA. However, molecular dynamics simulations performed on the PreQl riboswitch showed that TMAO destabilizes the tertiary riboswitch structure, leading
Elizabeth J. Denning +2 more
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Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure [PDF]
Nat Commun, 2019 Riboswitches are naturally occurring RNA aptamers that regulate gene expression by binding to specific small molecules. Riboswitches control the expression of essential bacterial genes and are important models for RNA-small molecule recognition. Here, we
C. Connelly +7 more
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A Comprehensive Review of Predicting Method of RNA Tertiary Structure
Computational Biology and Bioinformatics, 2021 In recent years, great progress has been made in the research of RNA function, and more and more RNA functions have been discovered. The function of RNA is highly dependent on its 3D structure, the RNA tertiary structure includes the RNA 3D structure and
Yurong Yang, Zhen-Dong Liu
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DEAD-box helicase proteins disrupt RNA tertiary structure through helix capture. [PDF]
PLoS Biology, 2014 DEAD-box helicase proteins accelerate folding and rearrangements of highly structured RNAs and RNA-protein complexes (RNPs) in many essential cellular processes. Although DEAD-box proteins have been shown to use ATP to unwind short RNA helices, it is not
Cynthia Pan +6 more
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