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Pseudoknots

A divide-and-conquer approach based on deep learning for long RNA secondary structure prediction: Focus on pseudoknots identification

Loïc Omnes, Eric Angel, Pierre Bartet, François Radvanyi, Fariza Tahi

published 25 Apr 2025

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Possible involvement of three-stemmed pseudoknots in regulating translational initiation in human mRNAs

Xiaolan Huang, Zhihua Du

published 22 Jul 2024

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Comparative analysis of RNA secondary structure accuracy on predicted RNA 3D models

Mandar Kulkarni, Jayaraman Thangappan, Indrajit Deb, Sangwook Wu

published 01 Sep 2023

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jViz.RNA 4.0—Visualizing pseudoknots and RNA editing employing compressed tree graphs

Boris Shabash, Kay C. Wiese

published 06 May 2019

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RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model

Hosna Jabbari, Ian Wark, Carlo Montemagno

published 05 Apr 2018

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Impact of the structural integrity of the three-way junction of adenovirus VA_I RNA on PKR inhibition

Edis Dzananovic, Astha, Grzegorz Chojnowski, Soumya Deo, Evan P. Booy, Pauline Padilla-Meier, Kevin McEleney, Janusz M. Bujnicki, Trushar R. Patel, Sean A. McKenna

published 20 Oct 2017

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Accurate Classification of RNA Structures Using Topological Fingerprints

Jiajie Huang, Kejie Li, Michael Gribskov

published 18 Oct 2016

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Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic

Amirhossein Manzourolajdad, Mileidy Gonzalez, John L. Spouge

published 29 Sep 2016

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Mutations Designed by Ensemble Defect to Misfold Conserved RNA Structures of Influenza A Segments 7 and 8 Affect Splicing and Attenuate Viral Replication in Cell Culture

Tian Jiang, Aitor Nogales, Steven F Baker, Luis Martinez-Sobrido, Douglas H Turner

published 07 Jun 2016

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Inhibition of Hepatitis C Virus in Mice by a Small Interfering RNA Targeting a Highly Conserved Sequence in Viral IRES Pseudoknot

Jae-Su Moon, Seung-Hoon Lee, Eun-Jung Kim, Hee Cho, Wooseong Lee, Geon-Woo Kim, Hyun-Ji Park, Seung-Woo Cho, Choongho Lee, Jong-Won Oh

published 11 Jan 2016

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

Yunqiang Bian, Jian Zhang, Jun Wang, Jihua Wang, Wei Wang

published 01 Jun 2015

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TBI Server: A Web Server for Predicting Ion Effects in RNA Folding

Yuhong Zhu, Zhaojian He, Shi-Jie Chen

published 23 Mar 2015

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Vfold: A Web Server for RNA Structure and Folding Thermodynamics Prediction

Xiaojun Xu, Peinan Zhao, Shi-Jie Chen

published 12 Sep 2014

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