Results 1 to 10 of about 517,188 (256)

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
doaj   +2 more sources

RNA independent fragment partition method based on deep learning for RNA secondary structure prediction [PDF]

Scientific Reports, 2023
The non-coding RNA secondary structure largely determines its function. Hence, accuracy in structure acquisition is of great importance. Currently, this acquisition primarily relies on various computational methods.
Qi Zhao, Qian Mao, Zheng Zhao, Wenxuan Yuan, Qiang He, Qixuan Sun, Yudong Yao, Xiaoya Fan   +7 more
doaj   +2 more sources

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
doaj   +4 more sources

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
doaj   +2 more sources

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
doaj   +2 more sources

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
doaj   +2 more sources

RNA secondary structure prediction with convolutional neural networks [PDF]

BMC Bioinformatics, 2022
Background Predicting the secondary, i.e. base-pairing structure of a folded RNA strand is an important problem in synthetic and computational biology.
Mehdi Saman Booy, Alexander Ilin, Pekka Orponen   +2 more
doaj   +2 more sources

A New Method of RNA Secondary Structure Prediction Based on Convolutional Neural Network and Dynamic Programming

Frontiers in Genetics, 2019
In recent years, obtaining RNA secondary structure information has played an important role in RNA and gene function research. Although some RNA secondary structures can be gained experimentally, in most cases, efficient, and accurate computational ...
Hao Zhang, Chunhe Zhang, Zhi Li, Cong Li, Xu Wei, Borui Zhang, Yuanning Liu   +6 more
doaj   +3 more sources

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
doaj   +2 more sources

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
doaj   +1 more source