Results 81 to 90 of about 14,400 (274)

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
doaj   +1 more source

HIV co-opts a cellular antiviral mechanism, activation of stress kinase PKR by its RNA, to enable splicing of rev/tat mRNA

Cell & Bioscience, 2023
Background Activation of RNA-dependent stress kinase PKR, especially by viral double-stranded RNA, induces eukaryotic initiation factor 2 α-chain (eIF2α) phosphorylation, attenuating thereby translation.
Lise Sarah Namer, Alex Harwig, Stephan P. Heynen, Atze T. Das, Ben Berkhout, Raymond Kaempfer   +5 more
doaj   +1 more source

Asymptotic Enumeration of RNA Structures with Pseudoknots [PDF]

Bulletin of Mathematical Biology, 2008
In this paper we present the asymptotic enumeration of RNA structures with pseudoknots. We develop a general framework for the computation of exponential growth rate and the sub exponential factors for $k$-noncrossing RNA structures. Our results are based on the generating function for the number of $k$-noncrossing RNA pseudoknot structures, ${\sf S}_k(
Christian M. Reidys, Emma Yu Jin
openaire   +4 more sources

Impact of the yeast S0/uS2-cluster ribosomal protein rpS21/eS21 on rRNA folding and the architecture of small ribosomal subunit precursors.

PLoS ONE, 2023
RpS0/uS2, rpS2/uS5, and rpS21/eS21 form a cluster of ribosomal proteins (S0-cluster) at the head-body junction near the central pseudoknot of eukaryotic small ribosomal subunits (SSU). Previous work in yeast indicated that S0-cluster assembly is required
Gisela Pöll, Joachim Griesenbeck, Herbert Tschochner, Philipp Milkereit   +3 more
doaj   +2 more sources

A Seeded Genetic Algorithm for RNA Secondary Structural Prediction with Pseudoknots [PDF]

, 2008
This work explores a new approach in using genetic algorithm to predict RNA secondary structures with pseudoknots. Since only a small portion of most RNA structures is comprised of pseudoknots, the majority of structural elements from an optimal ...
Pham, Ryan
core   +1 more source

DDX3 Regulates the Cap‐Independent Translation of the Japanese Encephalitis Virus via Its Interactions with PABP1 and the Untranslated Regions of the Viral Genome

Advanced Science, EarlyView.
Japanese encephalitis virus (JEV) employs a cap‐independent (CI) translation strategy to evade host translational shutoff. During the shut‐off of host cellular canonical translation, DEAD‐box protein 3 (DDX3) bind to JEV UTRs to establish a closed‐loop architecture, and its interaction with poly(A)‐binding protein 1 (PABP1) to form DDX3/PABP1/eIF4G ...
Chenxi Li, Linjie Zhang, Chenyang Tang, Xuan Chen, Jing Shi, Qingyu Li, Xue Jiao, Jinyao Guo, Bin Wang, Kefan Bu, Abdul Wahaab, Yuguo Yuan, Ming‐an Sun, Yanhua Li   +13 more
wiley   +1 more source

Loops in Canonical RNA Pseudoknot Structures [PDF]

Journal of Computational Biology, 2011
In this paper we compute the limit distributions of the numbers of hairpin-loops, interior-loops and bulges in k-noncrossing RNA structures. The latter are coarse grained RNA structures allowing for cross-serial interactions, subject to the constraint that there are at most k-1 mutually crossing arcs in the diagram representation of the molecule.
Nebel, Markus, M. Reidys, Christian, R. Wang, Rita   +2 more
openaire   +5 more sources

Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA

Viruses, 2017
The genomic RNA of the retrotransposon Ty1 is packaged as a dimer into virus-like particles. The 5′ terminus of Ty1 RNA harbors cis-acting sequences required for translation initiation, packaging and initiation of reverse transcription (TIPIRT).
Eric R. Gamache, Jung H. Doh, Justin Ritz, Alain Laederach, Stanislav Bellaousov, David H. Mathews, M. Joan Curcio   +6 more
doaj   +1 more source

Identification of the RNA Pseudoknot within the 3′ End of the Porcine Reproductive and Respiratory Syndrome Virus Genome as a Pathogen-Associated Molecular Pattern To Activate Antiviral Signaling via RIG-I and Toll-Like Receptor 3

Journal of Virology, 2018
Once infected by viruses, cells can detect pathogen-associated molecular patterns (PAMPs) on viral nucleic acid by host pattern recognition receptors (PRRs) to initiate the antiviral response.
Sha Xie, Xin-Xin Chen, S. Qiao, Rui Li, Yan-gang Sun, Shuangfei Xia, Lin-jian Wang, Xuegang Luo, R. Deng, E. Zhou, Gai-ping Zhang   +10 more
semanticscholar   +1 more source

Annexin, a Protein for All Seasons: From Calcium Dependent Membrane Metabolism to RNA Recognition

BioEssays, EarlyView.
Annexins are an important protein family traditionally well known to bind to phospholipids and to interact with various proteins in a calcium dependent way. More recently, it has been established that a feature common to the family is also to bind to RNA having a role in translation. In bies70019 article, Vedeler et al.
Anni Vedeler, Gian Gaetano Tartaglia, Annalisa Pastore   +2 more
wiley   +1 more source