Statistics of topological RNA structures
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Mathematical Biology"
DOI: 10.1007/s00285-016-1078-1
Abstract: In this paper we study properties of topological RNA structures, i.e. RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological structures having genus zero.… read more here.
Keywords: topological rna; rna; biology; statistics topological ... See more keywords
Functional RNA structures throughout the Hepatitis C Virus genome.
Sign Up to like & getrecommendations! Published in 2017 at "Current opinion in virology"
DOI: 10.1016/j.coviro.2017.04.007
Abstract: The single-stranded Hepatitis C Virus (HCV) genome adopts a set of elaborate RNA structures that are involved in every stage of the viral lifecycle. Recent advances in chemical probing, sequencing, and structural biology have facilitated… read more here.
Keywords: rna structures; rna; functional rna; hepatitis virus ... See more keywords
All-atom four-body knowledge-based statistical potential to distinguish native tertiary RNA structures from nonnative folds.
Sign Up to like & getrecommendations! Published in 2018 at "Journal of theoretical biology"
DOI: 10.1016/j.jtbi.2018.05.022
Abstract: Scientific breakthroughs in recent decades have uncovered the capability of RNA molecules to fulfill a wide array of structural, functional, and regulatory roles in living cells, leading to a concomitantly significant increase in both the… read more here.
Keywords: knowledge; rna structures; statistical potential; four body ... See more keywords
The roles of five conserved lentiviral RNA structures in HIV-1 replication.
Sign Up to like & getrecommendations! Published in 2018 at "Virology"
DOI: 10.1016/j.virol.2017.10.020
Abstract: The HIV-1 RNA genome contains complex structures with many structural elements playing regulatory roles during viral replication. A recent study has identified multiple RNA structures with unknown functions that are conserved among HIV-1 and two… read more here.
Keywords: conserved lentiviral; roles five; lentiviral rna; five conserved ... See more keywords
Design of a Temperature-Responsive Transcription Terminator.
Sign Up to like & getrecommendations! Published in 2018 at "ACS synthetic biology"
DOI: 10.1021/acssynbio.7b00356
Abstract: RNA structures regulate various steps in gene expression. Transcription in bacteria is typically terminated by stable hairpin structures. Translation initiation can be modulated by metabolite- or temperature-sensitive RNA structures, called riboswitches or RNA thermometers (RNATs),… read more here.
Keywords: transcription; temperature; temperature responsive; rna structures ... See more keywords
High-throughput determination of RNA structures
Sign Up to like & getrecommendations! Published in 2018 at "Nature Reviews Genetics"
DOI: 10.1038/s41576-018-0034-x
Abstract: RNA performs and regulates a diverse range of cellular processes, with new functional roles being uncovered at a rapid pace. Interest is growing in how these functions are linked to RNA structures that form in… read more here.
Keywords: throughput determination; determination rna; rna structures; high throughput ... See more keywords
RNA-Puzzles Round V: blind predictions of 23 RNA structures
Sign Up to like & getrecommendations! Published in 2024 at "Nature Methods"
DOI: 10.1038/s41592-024-02543-9
Abstract: RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We… read more here.
Keywords: round blind; blind predictions; predictions rna; puzzles round ... See more keywords
Investigating the role of RNA structures in transcriptional pausing using in vitro assays and in silico analyses
Sign Up to like & getrecommendations! Published in 2022 at "RNA Biology"
DOI: 10.1080/15476286.2022.2096794
Abstract: ABSTRACT Transcriptional pausing occurs across the bacterial genome but the importance of this mechanism is still poorly understood. Only few pauses were observed during the previous decades, leaving an important gap in understanding transcription mechanisms.… read more here.
Keywords: transcriptional pausing; rna; rna structures; pause sites ... See more keywords
Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac112
Abstract: Characterizing RNA structures and functions have mostly been focused on 2D, secondary and 3D, tertiary structures. Recent advances in experimental and computational techniques for probing or predicting RNA solvent accessibility make this 1D representation of… read more here.
Keywords: tertiary structures; structures functions; experimental computational; accessibility ... See more keywords
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac386
Abstract: Abstract Motivation The development of algorithms dedicated to RNA three-dimensional (3D) structures contributes to the demand for training, testing and benchmarking data. A reliable source of such data derived from computational prediction is the RNA-Puzzles… read more here.
Keywords: rna; rna structures; cleaned pdb; repository cleaned ... See more keywords
Vfold-Pipeline: a web server for RNA 3D structure prediction from sequences
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac426
Abstract: SUMMARY RNA 3D structures are critical for understanding their functions and for RNA-targeted drug design. However, experimental determination of RNA 3D structures is laborious and technically challenging, leading to the huge gap between the number… read more here.
Keywords: pipeline; rna structures; structure; structure prediction ... See more keywords