Results 81 to 90 of about 14,834 (261)

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

Rational Design Strategies for Stimuli‐Responsive DNAzymes Using Modified and Artificial Nucleotides

Chemistry – A European Journal, EarlyView.
Activity control of RNA‐cleaving DNAzymes in response to external stimuli has attracted growing interest for applications in DNA‐based diagnostics, therapeutics, and dynamic DNA nanotechnology. This review summarizes rational design strategies for stimuli‐responsive DNAzymes using modified or artificial nucleotides, including split and caged DNAzymes ...
Yusuke Takezawa, Mitsuhiko Shionoya
wiley   +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

Sequence analysis and genomic organization of Aphid lethal paralysis virus: a new member of the family Dicistroviridae [PDF]

, 2002
The complete nucleotide sequence of the genomic RNA of an aphid-infecting virus, Aphid lethal paralysis virus (ALPV), has been determined. The genome is 9812 nt in length and contains two long open reading frames (ORFs), which are separated by an ...
Clerivet, A., Dullemans, A.M., Heuvel, J.F.J.M., van den, Munster, M., van, Verbeek, M., Wilk, F., van der   +5 more
core   +2 more sources

Knotty: efficient and accurate prediction of complex RNA pseudoknot structures

Bioinform., 2018
Motivation The computational prediction of RNA secondary structure by free energy minimization has become an important tool in RNA research. However in practice, energy minimization is mostly limited to pseudoknot‐free structures or rather simple ...
H. Jabbari, Ian Wark, C. Montemagno, S. Will   +3 more
semanticscholar   +1 more source

SARS RNA pseudoknot [PDF]

Science-Business eXchange, 2011
In vitro studies identified an RNA-binding ligand that could help treat SARS-associated coronavirus infection.
openaire   +1 more source

Folding 3-Noncrossing RNA Pseudoknot Structures [PDF]

Journal of Computational Biology, 2009
32pages ...
Huang, Fenix W. D., Peng, Wade W. J., Reidys, Christian M.   +2 more
openaire   +3 more sources

Refining the Vertebrate Mitochondrial 12S rRNA Secondary Structure by Comparative Analysis

Integrative Zoology, EarlyView.
This flowchart outlines the comprehensive workflow of the study, integrating diverse bioinformatics tools (e.g., NCBI2GO, SSU‐align, bpRNA) and their sequential interactions. Key steps, such as data preprocessing, structural prediction, and evolutionary analysis, are depicted with their respective outputs (e.g., standardized records, consensus ...
Fengxia Li, Gengyun Niu, Renzeng Du, Kun Wan, David Roy Smith, Meicai Wei, Haihe Shi   +6 more
wiley   +1 more source

RNA secondary structure prediction from multi-aligned sequences [PDF]

, 2013
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution.
A Balik, A Pauli, A Wilm, A Wilm, AC Penn, AR Gruber, AS Richter, B Knudsen, B Knudsen, C Witwer, CB Do, D Jager, D Sankoff, D Wei, DH Mathews, DH Mathews, E Bindewald, E Freyhult, E Rivas, EJ Meer, H Kiryu, H Yonemoto, IA Qureshi, IL Hofacker, IL Hofacker, IV Novikova, J Ruan, J Spirollari, JG Underwood, JM Watts, JR Proctor, JS McCaskill, JT Low, K Katoh, K Sato, K Sato, K Sato, KM Wong, LE Carvalho, M Andronescu, M Andronescu, M Esteller, M Hamada, M Hamada, M Hamada, M Hamada, M Hamada, M Hamada, M Hamada, M Hamada, M Kertesz, ME Nebel, MS Andronescu, P Ge, PP Gardner, PS Pang, R Luck, RD Dowell, RJ Klein, S Washietl, S Washietl, S Washietl, S Washietl, SE Seemann, SE Seemann, SH Bernhart, SM Sahraeian, SW Burge, T Puton, T Xia, Y Kato, Z Sukosd   +71 more
core   +1 more source

A dynamic RNA loop in an IRES affects multiple steps of elongation factor-mediated translation initiation

eLife, 2015
Internal ribosome entry sites (IRESs) are powerful model systems to understand how the translation machinery can be manipulated by structured RNAs and for exploring inherent features of ribosome function.
Marisa D Ruehle, Haibo Zhang, Ryan M Sheridan, Somdeb Mitra, Yuanwei Chen, Ruben L Gonzalez Jr, Barry S Cooperman, Jeffrey S Kieft   +7 more
doaj   +1 more source