Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials

doi:10.1038/s42003-024-05952-w

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	Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials
	Gong, Tiansu 1,2; Ju, Fusong 1,2; Bu, Dongbo 1,2,3
	2024-03-09
发表期刊	COMMUNICATIONS BIOLOGY
卷号	7 期号:1 页码:13
摘要	Pseudoknots are key structure motifs of RNA and pseudoknotted RNAs play important roles in a variety of biological processes. Here, we present KnotFold, an accurate approach to the prediction of RNA secondary structure including pseudoknots. The key elements of KnotFold include a learned potential function and a minimum-cost flow algorithm to find the secondary structure with the lowest potential. KnotFold learns the potential from the RNAs with known structures using an attention-based neural network, thus avoiding the inaccuracy of hand-crafted energy functions. The specially designed minimum-cost flow algorithm used by KnotFold considers all possible combinations of base pairs and selects from them the optimal combination. The algorithm breaks the restriction of nested base pairs required by the widely used dynamic programming algorithms, thus enabling the identification of pseudoknots. Using 1,009 pseudoknotted RNAs as representatives, we demonstrate the successful application of KnotFold in predicting RNA secondary structures including pseudoknots with accuracy higher than the state-of-the-art approaches. We anticipate that KnotFold, with its superior accuracy, will greatly facilitate the understanding of RNA structures and functionalities. Presenting KnotFold, an application for accurately predicting RNA secondary structures, including pseudoknots.
DOI	10.1038/s42003-024-05952-w
收录类别	SCI
语种	英语
资助项目	the National Key Research and Development Program of China (2020YFA0907000), and the National Natural Science Foundation of China (32370657, 32271297, 82130055, 62072435)[2020YFA0907000] ; National Key Research and Development Program of China[32370657] ; National Key Research and Development Program of China[32271297] ; National Key Research and Development Program of China[82130055] ; National Key Research and Development Program of China[62072435] ; National Natural Science Foundation of China ; ICT Computer-X center, Chinese Academy of Sciences
WOS研究方向	Life Sciences & Biomedicine - Other Topics ; Science & Technology - Other Topics
WOS类目	Biology ; Multidisciplinary Sciences
WOS记录号	WOS:001185102800004
出版者	NATURE PORTFOLIO
引用统计	被引频次：1[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/38799
专题	中国科学院计算技术研究所
通讯作者	Bu, Dongbo
作者单位	1.Chinese Acad Sci, Key Lab Intelligent Informat Proc, Inst Comp Technol, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100190, Peoples R China 3.Henan Acad Sci, Cent China Artificial Intelligence Res Inst, Zhengzhou 450046, Henan, Peoples R China
推荐引用方式 GB/T 7714	Gong, Tiansu,Ju, Fusong,Bu, Dongbo. Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials[J]. COMMUNICATIONS BIOLOGY,2024,7(1):13.
APA	Gong, Tiansu,Ju, Fusong,&Bu, Dongbo.(2024).Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials.COMMUNICATIONS BIOLOGY,7(1),13.
MLA	Gong, Tiansu,et al."Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials".COMMUNICATIONS BIOLOGY 7.1(2024):13.