Results 101 to 110 of about 14,795 (267)
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
RNA structure prediction: progress and perspective
, 2014 Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures.
Shi, Ya-Zhou +3 more
core +1 more source
Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA Homology Search: Overview and New Results [PDF]
, 2008 Systematic research on noncoding RNAs (ncRNAs) has revealed that many ncRNAs are actively involved in various biological networks. Therefore, in order to fully understand the mechanisms of these networks, it is crucial to understand the roles of ncRNAs ...
Vaidyanathan, P. P., Yoon, Byung-Jun
core +2 more sources
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
Genes to Cells, Volume 31, Issue 1, January 2026.DiCleavePlus integrates pre‐miRNA sequence and secondary structure information through Transformer‐based feature extraction to predict Dicer cleavage site positions with high accuracy. The model converts Dicer cleavage prediction into a multi‐class task, enabling precise and robust identification of cleavage intervals across human pre‐miRNAs.
Lixuan Mu, Tatsuya Akutsu
wiley +1 more source
SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration
Algorithms for Molecular BiologyMotivation Computational RNA secondary structure prediction by free energy minimization is indispensable for analyzing structural RNAs and their interactions.
Mateo Gray +2 more
doaj +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
Insights into factorless translational initiation by the tRNA-like pseudoknot domain of a viral IRES. [PDF]
PLoS ONE, 2012 The intergenic region internal ribosome entry site (IGR IRES) of the Dicistroviridae family adopts an overlapping triple pseudoknot structure to directly recruit the 80S ribosome in the absence of initiation factors.
Hilda H T Au, Eric Jan
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