Results 141 to 150 of about 14,795 (267)

ENTRNA: a framework to predict RNA foldability

open access: yesBMC 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

open access: yesBMC 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

open access: yesNature 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

open access: yesPLoS 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]

open access: bronze, 1999
Timothy S. Wadkins   +4 more
openalex   +1 more source

Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding.

open access: yesPLoS 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

open access: yesMolecular 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

The RNA pseudoknots in foot-and-mouth disease virus are dispensable for genome replication, but essential for the production of infectious virus

open access: gold, 2022
Joseph C. Ward   +14 more
openalex   +2 more sources

Prediction of RNA pseudoknots by Monte Carlo simulations

open access: yes, 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

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