Results 111 to 120 of about 14,834 (261)
Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage
Nature Chemical Biology, 2016 The field of small self-cleaving nucleolytic ribozymes has been invigorated by the recent discovery of the twister, twister-sister, pistol and hatchet ribozymes.
A. Ren +7 more
semanticscholar +1 more source
The RNA‐Puzzles Assessments of RNA‐Only Targets in CASP16
Proteins: Structure, Function, and Bioinformatics, Volume 94, Issue 1, Page 218-229, January 2026.ABSTRACT RNA‐Puzzles was launched in 2011 as a collaborative effort dedicated to advancing and improving RNA 3D structure prediction. The automatic evaluation protocols for comparisons between prediction and experiment developed within RNA‐Puzzles are applied to the 2024 CASP16 competition.
Eric Westhof +3 more
wiley +1 more source
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 +1 more
openaire +2 more sources
Folding thermodynamics of pseudoknotted chain conformations [PDF]
The Journal of Chemical Physics, 2006 We develop a statistical mechanical framework for the folding thermodynamics of pseudoknotted structures. As applications of the theory, we investigate the folding stability and the free energy landscapes for both the thermal and the mechanical unfolding of pseudoknotted chains.
Zoia, Kopeikin, Shi-Jie, Chen
openaire +2 more sources
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 +3 more
doaj +1 more source
A Graph Grammar for Modelling RNA Folding
, 2016 We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the global behaviour ...
Mamuye, Adane Letta +2 more
core +2 more sources
Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot
Nucleic Acids Research, 2017 Frameshifting is an essential process that regulates protein synthesis in many viruses. The ribosome may slip backward when encountering a frameshift motif on the messenger RNA, which usually contains a pseudoknot structure involving tertiary base pair ...
Yu-Ting Chen +8 more
semanticscholar +1 more source
Practical Outcomes From CASP16 for Users in Need of Biomolecular Structure Prediction
Proteins: Structure, Function, and Bioinformatics, Volume 94, Issue 1, Page 435-446, January 2026.ABSTRACT The 16th Critical Assessment of Structure Prediction benchmarked advancements in biomolecular modeling, particularly in the context of AlphaFold 2 and 3 systems. Protein monomer and domain prediction is largely solved, with barely any space for further improvements at the backbone level except for very specific details, irregular secondary ...
Luciano A. Abriata, Matteo Dal Peraro
wiley +1 more source
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 +6 more
doaj +1 more source
Nucleic Acids Research, 2018 Telomerase adds telomeric repeats to chromosome ends by processive copying of a template within the telomerase RNA bound to telomerase reverse transcriptase.
A. Deshpande, K. Collins
semanticscholar +1 more source