ENTRNA: a framework to predict RNA foldability
BMC Bioinformatics, 2019 Background RNA molecules play many crucial roles in living systems. The spatial complexity that exists in RNA structures determines their cellular functions.
Congzhe Su +4 more
doaj +1 more source
antaRNA – Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization
BMC Bioinformatics, 2015 Many functional RNA molecules fold into pseudoknot structures, which are often essential for the formation of an RNA’s 3D structure. Currently the design of RNA molecules, which fold into a specific structure (known as RNA inverse folding) within ...
Robert Kleinkauf +3 more
semanticscholar +1 more source
Nanopore electric snapshots of an RNA tertiary folding pathway
Nature Communications, 2017 While RNA folding is critical for its function, study of this process is challenging. Here, the authors combine nanopore single-molecule manipulation with theoretical analysis to follow the folding of an RNA pseudoknot, monitoring the intermediate states
Xinyue Zhang +9 more
doaj +1 more source
Free Energy Landscape and Multiple Folding Pathways of an H-Type RNA Pseudoknot
PLoS ONE, 2015 How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias ...
Yunqiang Bian +4 more
semanticscholar +1 more source
A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes [PDF]
, 1999 Timothy S. Wadkins +4 more
openalex +1 more source
Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding.
PLoS ONE, 2007 Predicting RNA secondary structure is often the first step to determining the structure of RNA. Prediction approaches have historically avoided searching for pseudoknots because of the extreme combinatorial and time complexity of the problem.
Wayne K Dawson +2 more
doaj +1 more source
Absolute quantification of translational regulation and burden using combined sequencing approaches
Molecular Systems Biology, 2019 Translation of mRNAs into proteins is a key cellular process. Ribosome binding sites and stop codons provide signals to initiate and terminate translation, while stable secondary mRNA structures can induce translational recoding events.
Thomas E Gorochowski +5 more
doaj +1 more source
TT2NE: A novel algorithm to predict RNA secondary structures with\n pseudoknots [PDF]
, 2010 Michaël Bon, Henri Orland
openalex +3 more sources
Prediction of RNA pseudoknots by Monte Carlo simulations
, 2004 In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams.
Orland, H., Vernizzi, G., Zee, A.
core +1 more source