Results 141 to 150 of about 14,834 (261)

The DEAH-box Helicase Dhr1 Dissociates U3 from the Pre-rRNA to Promote Formation of the Central Pseudoknot

PLoS Biology, 2015
In eukaryotes, the highly conserved U3 small nucleolar RNA (snoRNA) base-pairs to multiple sites in the pre-ribosomal RNA (pre-rRNA) to promote early cleavage and folding events.
Richa Sardana, Xin Liu, S. Granneman, Jieyi Zhu, Michael Gill, Ophelia Papoulas, E. Marcotte, D. Tollervey, C. C. Correll, Arlen W. Johnson   +9 more
semanticscholar   +1 more source

antaRNA – Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization

BMC Bioinformatics, 2015
Many functional RNA molecules fold into pseudoknot structures, which are often essential for the formation of an RNA’s 3D structure. Currently the design of RNA molecules, which fold into a specific structure (known as RNA inverse folding) within ...
Robert Kleinkauf, Torsten Houwaart, R. Backofen, Martin Mann   +3 more
semanticscholar   +1 more source

ENTRNA: a framework to predict RNA foldability

BMC Bioinformatics, 2019
Background RNA molecules play many crucial roles in living systems. The spatial complexity that exists in RNA structures determines their cellular functions.
Congzhe Su, Jeffery D. Weir, Fei Zhang, Hao Yan, Teresa Wu   +4 more
doaj   +1 more source

An efficient simulated annealing algorithm for the RNA secondary structure prediction with Pseudoknots

BMC Genomics, 2019
Background RNA pseudoknot structures play an important role in biological processes. However, existing RNA secondary structure prediction algorithms cannot predict the pseudoknot structure efficiently.
Zhang Kai, Wang Yuting, Lv Yulin, Liu Jun, He Juanjuan   +4 more
doaj   +1 more source

Free Energy Landscape and Multiple Folding Pathways of an H-Type RNA Pseudoknot

PLoS ONE, 2015
How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias ...
Yunqiang Bian, Jian Zhang, Jun Wang, Jihua Wang, Wei Wang   +4 more
semanticscholar   +1 more source

Nanopore electric snapshots of an RNA tertiary folding pathway

Nature Communications, 2017
While RNA folding is critical for its function, study of this process is challenging. Here, the authors combine nanopore single-molecule manipulation with theoretical analysis to follow the folding of an RNA pseudoknot, monitoring the intermediate states
Xinyue Zhang, Dong Zhang, Chenhan Zhao, Kai Tian, Ruicheng Shi, Xiao Du, Andrew J. Burcke, Jing Wang, Shi-Jie Chen, Li-Qun Gu   +9 more
doaj   +1 more source

Contributions of Pseudoknots and Protein SmpB to the Structure and Function of tmRNA in trans-Translation [PDF]

, 2004
Iwona K. Wower, Christian Zwieb, Jacek Wower   +2 more
openalex   +1 more source

Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions [PDF]

, 2023
Xunxun Wang, Ya-Lan Tan, Shixiong Yu, Ya-Zhou Shi, Zhi-Jie Tan   +4 more
openalex   +1 more source

Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding.

PLoS ONE, 2007
Predicting RNA secondary structure is often the first step to determining the structure of RNA. Prediction approaches have historically avoided searching for pseudoknots because of the extreme combinatorial and time complexity of the problem.
Wayne K Dawson, Kazuya Fujiwara, Gota Kawai   +2 more
doaj   +1 more source

RNA Pseudoknots Obtained by Means of Knowledge-Based Interaction Potentials [PDF]

, 2012
Mauricio D. Carbajal‐Tinoco
openalex   +1 more source