Results 151 to 160 of about 14,400 (274)
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
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
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
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
Partitioning RNAs into pseudonotted and pseudoknot-free regions modeled as Dual Graphs [PDF]
arXiv, 2016 Dual graphs have been applied to model RNA secondary structures. The purpose of the paper is two-fold: we present new graph-theoretic properties of dual graphs to validate the further analysis and classification of RNAs using these topological representations; we also present a linear-time algorithm to partition dual graphs into topological components ...
arxiv
Frameshifting RNA pseudoknots: Structure and mechanism
Virus Research, 2009 Programmed ribosomal frameshifting (PRF) is one of the multiple translational recoding processes that fundamentally alters triplet decoding of the messenger RNA by the elongating ribosome. The ability of the ribosome to change translational reading frames in the -1 direction (-1 PRF) is employed by many positive strand RNA viruses, including ...
Peter V. Cornish, David P. Giedroc
openaire +3 more sources
BMC Genomics, 2019 Background RNA pseudoknot structures play an important role in biological processes. However, existing RNA secondary structure prediction algorithms cannot predict the pseudoknot structure efficiently.
Zhang Kai +4 more
doaj +1 more source
The Influenza A PB1-F2 and N40 Start Codons Are Contained within an RNA Pseudoknot.
Biochemistry, 2015 Influenza A is a negative-sense RNA virus with an eight-segment genome. Some segments encode more than one polypeptide product, but how the virus accesses alternate internal open reading frames (ORFs) is not completely understood. In segment 2, ribosomal
S. Priore +3 more
semanticscholar +1 more source
Nucleic Acids Research, 2014 RydC pseudoknot aided by Hfq is a dynamic regulatory module. We report that RydC reduces expression of curli-specific gene D transcription factor required for adhesion and biofilm production in enterobacteria.
V. Bordeau, B. Felden
semanticscholar +1 more source
Bipartite signal for read-through suppression in murine leukemia virus mRNA: an eight-nucleotide purine-rich sequence immediately downstream of the gag termination codon followed by an RNA pseudoknot [PDF]
, 1992 Yan Feng +3 more
openalex +1 more source