Results 1 to 10 of about 10,995,303 (306)

RNA secondary structure factorization in prime tangles [PDF]

BMC Bioinformatics, 2022
Background Due to its key role in various biological processes, RNA secondary structures have always been the focus of in-depth analyses, with great efforts from mathematicians and biologists, to find a suitable abstract representation for modelling its ...
Daniele Marchei, Emanuela Merelli
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Comparative analysis of RNA secondary structure accuracy on predicted RNA 3D models. [PDF]

PLoS ONE, 2023
RNA structure is conformationally dynamic, and accurate all-atom tertiary (3D) structure modeling of RNA remains challenging with the prevailing tools. Secondary structure (2D) information is the standard prerequisite for most RNA 3D modeling.
Mandar Kulkarni, Jayaraman Thangappan, Indrajit Deb, Sangwook Wu   +3 more
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RNA secondary structure prediction by conducting multi-class classifications [PDF]

Computational and Structural Biotechnology Journal
Generating valid predictions of RNA secondary structures is challenging. Several deep learning methods have been developed for predicting RNA secondary structures.
Jiyuan Yang, Kengo Sato, Martin Loza, Sung-Joon Park, Kenta Nakai   +4 more
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StructRMDB: A database of RNA modification sites that affect RNA secondary structure [PDF]

Computational and Structural Biotechnology Journal
Post-transcriptional RNA modifications, prevalent in multiple RNA species such as mRNA, rRNA, and tRNA, play a significant role in biological processes by altering RNA structures.
Ziyan Zhang, Xuan Wang, Jingxian Zhou, Jia Meng, Bowen Song, Yuxin Liang, Yuheng Cai, Jiongming Ma   +7 more
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NTFold: Structure-Sensing Nucleotide Attention Learning for RNA Secondary Structure Prediction [PDF]

Sensors
Determining RNA secondary structures is a fundamental challenge in computational biology and molecular sensing. Experimental techniques such as X-ray crystallography, nuclear magnetic resonance, and cryo-electron microscopy can reveal RNA structures with
Kangjun Jin, Zhuo Zhang, Guipeng Lan, Shuai Xiao, Jiachen Yang   +4 more
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Analysis of the abundance and diversity of RNA secondary structure elements in RNA viruses using the RNAsselem Python package [PDF]

Scientific Reports
Recent advancements in experimental and computational methods for RNA secondary structure detection have revealed the crucial role of RNA structural elements in diverse molecular processes within living cells.
Fedor M. Kazanov, Evgenii V. Matveev, Gennady V. Ponomarev, Dmitry N. Ivankov, Marat D. Kazanov   +4 more
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Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models

Viruses, 2021
Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing
Simón Poblete, Horacio V. Guzman
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Long non-coding RNA-polycomb intimate rendezvous [PDF]

Open Biology, 2020
The interaction between polycomb-repressive complexes 1/2 (PRC1/2) and long non-coding RNA (lncRNA), such as the X inactive specific transcript Xist and the HOX transcript antisense RNA (HOTAIR), has been the subject of intense debate.
Andrea Cerase, Gian Gaetano Tartaglia
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RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix

BMC Bioinformatics, 2021
Background The functions of RNA molecules are mainly determined by their secondary structures. These functions can also be predicted using bioinformatic tools that enable the alignment of multiple RNAs to determine functional domains and/or classify RNA ...
Tomasz Woźniak, Małgorzata Sajek, Jadwiga Jaruzelska, Marcin Piotr Sajek   +3 more
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SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability

Computational and Structural Biotechnology Journal, 2022
RNA secondary structures can carry out essential cellular functions alone or interact with one another to form the hierarchical tertiary structures.
Tzu-Hsien Yang, Yu-Cian Lin, Min Hsia, Zhan-Yi Liao   +3 more
doaj   +1 more source