Results 71 to 80 of about 14,400 (274)

RNA-Puzzles Round IV:3D structure predictions of four ribozymes and two aptamers [PDF]

, 2020
International audienceRNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of ...
Adamiak, Ryszard W., Antczak, Maciej, Batey, Robert T., Boniecki, Michal J., Bujnicki, Janusz M., Chen, Shi-Jie, Cheng, Clarence Yu, Cheng, Yi, Chou, Fang-Chieh, Das, Rhiju, Ding, Feng, Dokholyan, Nikolay V., Geniesse, Caleb, Golden, Barbara L., Huang, Lin, Jiang, Yangwei, Joshi, Astha, Krokhotin, Andrey, Lilley, David M., Liu, Yijin, Magnus, Marcin, Mailhot, Olivier, Major, Francois, Mann, Thomas H., Miao, Zhichao, Patel, Dinshaw J., Piatkowski, Pawel, Pluta, Radoslaw, Popenda, Mariusz, Ren, Aiming, Sarzynska, Joanna, Sun, Lizhen, Szachniuk, Marta, Tian, Siqi, Wang, Jian, Wang, Jun, Watkins, Andrew M., Westhof, Eric, Wiedemann, Jakub, Xiao, Yi, Xu, Xiaojun, Yesselman, Joseph D., Zhang, Dong, Zhang, Yi, Zhang, Zhenzhen, Zhao, Chenhan, Zhao, Peinan, Zhou, Yuanzhe, Zok, Tomasz, Zyla, Adriana   +49 more
core   +3 more sources

The 3′ Untranslated Region of a Plant Viral RNA Directs Efficient Cap-Independent Translation in Plant and Mammalian Systems

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, Mariko S. Peterson, Sung Ki Cho, Zhaohui Wang, Alice Hui, Aurélie M. Rakotondrafara, Krzysztof Treder, Cathy L. Miller, W. Allen Miller   +8 more
doaj   +1 more source

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, Megan G. Oskam, Sophie Overbeek, René C.L. Olsthoorn   +3 more
doaj   +1 more source

Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements. [PDF]

, 2017
In single stranded (+)-sense RNA viruses, RNA structural elements (SEs) play essential roles in the infection process from replication to encapsidation.
Aviran, Sharon, Choudhary, Krishna, Lucks, Julius B, Perry, Keith L, Thompson, Jeremy R, Watters, Kyle E   +5 more
core   +2 more sources

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, Surajit Chatterjee, May Daher, N. Walter   +3 more
semanticscholar   +1 more source

Psybrackets, pseudoknots and singular knots

Journal of Knot Theory and Its Ramifications, 2023
We introduce algebraic structures known as psybrackets and use them to define invariants of pseudoknots and singular knots and links. Psybrackets are Niebrzydowski tribrackets with additional structure inspired by the Reidemeister moves for pseudoknots and singular knots. Examples and computations are provided.
Jeong, Suhyeon, Kim, Jieon, Nelson, Sam
openaire   +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

Classifying RNA pseudoknotted structures

Theoretical Computer Science, 2004
AbstractComputational prediction of the minimum free energy (mfe) secondary structure of an RNA molecule from its base sequence is valuable in understanding the structure and function of the molecule. Since the general problem of predicting pseudoknotted secondary structures is NP-hard, several algorithms have been proposed that find the mfe secondary ...
Condon, Anne, Davy, Beth, Rastegari, Baharak, Zhao, Shelly, Tarrant, Finbarr   +4 more
openaire   +4 more sources

A procedure for RNA pseudoknot prediction [PDF]

Bioinformatics, 1992
The RNA pseudoknot has been proposed as a significant structural motif in a wide range of biological processes of RNAs. A pseudoknot involves intramolecular pairing of bases in a hairpin loop with bases outside the stem of the loop to form a second stem and loop region.
Shu-Yun Le, Jacob V. Maizel, Jih-Hsiang Chen   +2 more
openaire   +3 more sources

Pseudoknots in RNA secondary structures

Proceedings of the fourth annual international conference on Computational molecular biology, 2000
<p>RNA molecules are sequences of nucleotides that serve as more than mere intermediaries between DNA and proteins, e.g. as catalytic molecules. Computational prediction of RNA secondary structure is among the few structure prediction problems that can be solved satisfactorily in polynomial time. Most work has been done to predict structures that
Rune B. Lyngsø, Christian N. S. Pedersen   +1 more
openaire   +4 more sources