Deep generalizable prediction of RNA secondary structure via base pair motif energy
文献类型：期刊论文
| 作者 | Zhu, Heqin1,2,3; Tang, Fenghe1,2,3; Quan, Quan4; Chen, Ke1,2; Xiong, Peng1,2; Zhou, S. Kevin1,2,3,5,6 |
| 刊名 | NATURE COMMUNICATIONS
 |
| 出版日期 | 2025-07-01 |
| 卷号 | 16期号:1页码:13 |
| DOI | 10.1038/s41467-025-60048-1 |
| 英文摘要 | 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. |
| 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 |
| 语种 | 英语 |
| WOS记录号 | WOS:001523450500025 |
| 出版者 | NATURE PORTFOLIO |
| 源URL | [http://119.78.100.204/handle/2XEOYT63/42022]  |
| 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. |
入库方式： OAI收割
来源：计算技术研究所
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