Deep generalizable prediction of RNA secondary structure via base pair motif energy

doi:10.1038/s41467-025-60048-1

	Deep generalizable prediction of RNA secondary structure via base pair motif energy
	Zhu, Heqin 1,2,3; Tang, Fenghe 1,2,3; Quan, Quan 4; Chen, Ke 1,2; Xiong, Peng 1,2; Zhou, S. Kevin 1,2,3,5,6
	2025-07-01
发表期刊	NATURE COMMUNICATIONS
卷号	16 期号:1 页码:13
摘要	Deep learning methods have demonstrated great performance for RNA secondary structure prediction. However, generalizability is a common unsolved issue on unseen out-of-distribution RNA families, which hinders further improvement of the accuracy and robustness of deep learning methods. Here we construct a base pair motif library that enumerates the complete space of the locally adjacent three-neighbor base pair and records the thermodynamic energy of corresponding base pair motifs through de novo modeling of tertiary structures, and we further develop a deep learning approach for RNA secondary structure prediction, named BPfold, which learns relationship between RNA sequence and the energy map of base pair motif. Experiments on sequence-wise and family-wise datasets have demonstrated the great superiority of BPfold compared to other state-of-the-art approaches in accuracy and generalizability. We hope this work contributes to integrating physical priors and deep learning methods for the further discovery of RNA structures and functionalities.
DOI	10.1038/s41467-025-60048-1
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China (National Science Foundation of China)[62271465] ; National Natural Science Foundation of China (National Science Foundation of China)[32370581] ; National Natural Science Foundation of China[SYG202338] ; Suzhou Basic Research Program
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:001523450500025
出版者	NATURE PORTFOLIO
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/42023
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Xiong, Peng; Zhou, S. Kevin
作者单位	1.Univ Sci & Technol China USTC, Sch Biomed Engn, Div Life Sci & Med, Hefei 230026, Anhui, Peoples R China 2.USTC, Suzhou Inst Adv Res, Suzhou 215123, Jiangsu, Peoples R China 3.USTC, Suzhou Inst Adv Res, Ctr Med Imaging Robot Analyt Comp Learning MIRACLE, Suzhou 215123, Jiangsu, Peoples R China 4.Chinese Acad Sci, Key Lab Intelligent Informat Proc, Inst Comp Technol, Beijing 100190, Peoples R China 5.Jiangsu Prov Key Lab Multimodal Digital Twin Techn, Suzhou 215123, Jiangsu, Peoples R China 6.USTC, State Key Lab Precis & Intelligent Chem, Hefei 230026, Anhui, Peoples R China
推荐引用方式 GB/T 7714	Zhu, Heqin,Tang, Fenghe,Quan, Quan,et al. Deep generalizable prediction of RNA secondary structure via base pair motif energy[J]. NATURE COMMUNICATIONS,2025,16(1):13.
APA	Zhu, Heqin,Tang, Fenghe,Quan, Quan,Chen, Ke,Xiong, Peng,&Zhou, S. Kevin.(2025).Deep generalizable prediction of RNA secondary structure via base pair motif energy.NATURE COMMUNICATIONS,16(1),13.
MLA	Zhu, Heqin,et al."Deep generalizable prediction of RNA secondary structure via base pair motif energy".NATURE COMMUNICATIONS 16.1(2025):13.