Results 71 to 80 of about 14,834 (261)
Predicting RNA pseudoknot folding thermodynamics [PDF]
Nucleic Acids Research, 2006 Based on the experimentally determined atomic coordinates for RNA helices and the self-avoiding walks of the P (phosphate) and C4 (carbon) atoms in the diamond lattice for the polynucleotide loop conformations, we derive a set of conformational entropy parameters for RNA pseudoknots.
Cao, Song, Chen, Shi-Jie
openaire +2 more sources
Psyquandles, Singular Knots and Pseudoknots [PDF]
Tokyo Journal of Mathematics, 2019 20 ...
NELSON, Sam +2 more
openaire +4 more sources
RNA denaturation: excluded volume, pseudoknots and transition scenarios [PDF]
, 2003 A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition ...
A. L. Stella +12 more
core +1 more source
Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production
Viruses, 2013 In previous studies, differences in the amount of genomic and subgenomic RNA produced by coronaviruses with mutations in the programmed ribosomal frameshift signal of ORF1a/b were observed.
Ewan P. Plant +4 more
doaj +1 more source
JACS AuIn the 3′ untranslated region of the SARS-CoV-2 virus RNA genome, genomic RNA replication is initiated in the highly conserved region called 3′PK, containing three stem structures (P1pk, P2, and P5).
Takako Ohyama +3 more
semanticscholar +1 more source
Sequence-structure relations of pseudoknot RNA
BMC Bioinformatics, 2009 Background The analysis of sequence-structure relations of RNA is based on a specific notion and folding of RNA structure. The notion of coarse grained structure employed here is that of canonical RNA pseudoknot contact-structures with at most two ...
Li Linda YM +2 more
doaj +1 more source
Pathogens, 2019 Many plant viral RNA genomes lack a 5′ cap, and instead are translated via a cap-independent translation element (CITE) in the 3′ untranslated region (UTR).
Jelena J. Kraft +8 more
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Investigating the correlation between Xrn1-resistant RNAs and frameshifter pseudoknots
RNA Biology, 2023 Xrn1-resistant RNA structures are multifunctional elements employed by an increasing number of RNA viruses. One of such elements is the coremin motif, discovered in plant virus RNAs, of which the structure has been hypothesized to form a yet unelucidated
Ivar W. Dilweg +3 more
doaj +1 more source
Efficient known ncRNA search including pseudoknots
BMC Bioinformatics, 2013 Background Searching for members of characterized ncRNA families containing pseudoknots is an important component of genome-scale ncRNA annotation. However, the state-of-the-art known ncRNA search is based on context-free grammar (CFG), which cannot ...
Yuan Cheng, Sun Yanni
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Protein unties the pseudoknot: S1-mediated unfolding of RNA higher order structure
Nucleic Acids Research, 2019 Ribosomal protein S1 plays important roles in the translation initiation step of many Escherichia coli mRNAs, particularly those with weak Shine-Dalgarno sequences or structured 5′ UTRs, in addition to a variety of cellular processes beyond the ribosome.
P. E. Lund +3 more
semanticscholar +1 more source