FARFAR2: improved de novo rosetta prediction of complex global RNA folds
Predicting RNA three-dimensional structures from sequence could accelerate
understanding of the growing number of RNA molecules being discovered across biology …
understanding of the growing number of RNA molecules being discovered across biology …
LinearFold: linear-time approximate RNA folding by 5'-to-3'dynamic programming and beam search
Motivation Predicting the secondary structure of an ribonucleic acid (RNA) sequence is
useful in many applications. Existing algorithms [based on dynamic programming] suffer …
useful in many applications. Existing algorithms [based on dynamic programming] suffer …
3D RNA and functional interactions from evolutionary couplings
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far
outpaces the research on the structure and functional interactions of these RNA gene …
outpaces the research on the structure and functional interactions of these RNA gene …
The ViennaRNA web services
The ViennaRNA package is a widely used collection of programs for thermodynamic RNA
secondary structure prediction. Over the years, many additional tools have been developed …
secondary structure prediction. Over the years, many additional tools have been developed …
An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs
T Ohyama, H Takahashi, H Sharma… - Nucleic Acids …, 2020 - academic.oup.com
Long non-coding RNAs (lncRNAs) are attracting widespread attention for their emerging
regulatory, transcriptional, epigenetic, structural and various other functions. Comprehensive …
regulatory, transcriptional, epigenetic, structural and various other functions. Comprehensive …
An aptamer-based biosensor for direct, label-free detection of melamine in raw milk
N Kaneko, K Horii, J Akitomi, S Kato, I Shiratori, I Waga - Sensors, 2018 - mdpi.com
Melamine, a nitrogen-rich compound, has been used as a food and milk additive to falsely
increase the protein content. However, melamine is toxic, and high melamine levels in food …
increase the protein content. However, melamine is toxic, and high melamine levels in food …
Model-free RNA sequence and structure alignment informed by SHAPE probing reveals a conserved alternate secondary structure for 16S rRNA
Discovery and characterization of functional RNA structures remains challenging due to
deficiencies in de novo secondary structure modeling. Here we describe a dynamic …
deficiencies in de novo secondary structure modeling. Here we describe a dynamic …
Differences in integron cassette excision dynamics shape a trade-off between evolvability and genetic capacitance
Integrons ensure a rapid and “on demand” response to environmental stresses driving
bacterial adaptation. They are able to capture, store, and reorder functional gene cassettes …
bacterial adaptation. They are able to capture, store, and reorder functional gene cassettes …
Expansion segments in bacterial and archaeal 5S ribosomal RNAs
VG Stepanov, GE Fox - RNA, 2021 - rnajournal.cshlp.org
The large ribosomal RNAs of eukaryotes frequently contain expansion sequences that add
to the size of the rRNAs but do not affect their overall structural layout and are compatible …
to the size of the rRNAs but do not affect their overall structural layout and are compatible …
The UEA small RNA workbench: a suite of computational tools for small RNA analysis
RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism
mediated by short, typically 20–24 nt in length, noncoding RNAs known as small RNAs …
mediated by short, typically 20–24 nt in length, noncoding RNAs known as small RNAs …