RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction
文献类型：期刊论文
| 作者 | Wang, Yunxia2; Chen, Zhen2; Pan, Ziqi2; Huang, Shijie2; Liu, Jin2; Xia, Weiqi2; Zhang, Hongning2; Zheng, Mingyue3 ; Li, Honglin1,2; Hou, Tingjun2
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| 刊名 | NUCLEIC ACIDS RESEARCH
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| 出版日期 | 2023-05-11 |
| 页码 | 11 |
| ISSN号 | 0305-1048 |
| DOI | 10.1093/nar/gkad404 |
| 通讯作者 | Zhu, Feng(zhufeng@zju.edu.cn) |
| 英文摘要 | Ribonucleic acids (RNAs) involve in various physiological/pathological processes by interacting with proteins, compounds, and other RNAs. A variety of powerful computational methods have been developed to predict such valuable interactions. However, all these methods rely heavily on the `digitalization' (also known as encoding') of RNA-associated interacting pairs into a computer-recognizable descriptor. In other words, it is urgently needed to have a powerful tool that can not only represent each interacting partner but also integrate both partners into a computer-recognizable interaction. Herein, RNAincoder (deep learning-based encoder for RNA-associated interactions) was therefore proposed to (a) provide a comprehensive collection of RNA encoding features, (b) realize the representation of any RNA-associated interaction based on a well-established deep learning-based embedding strategy and (c) enable large-scale scanning of all possible feature combinations to identify the one of optimal performance in RNA-associated interaction prediction. The effectiveness of RNAincoder was extensively validated by case studies on benchmark datasets. All in all, RNAincoder is distinguished for its capability in providing a more accurate representation of RNA-associated interactions, which makes it an indispensable complement to other available tools. RNAincoder can be accessed at https:'rnaincoder/ [GRAPHICS] . |
| WOS关键词 | WEB SERVER ; PREDICTION ; SEQUENCE ; PROTEINS ; FAMILY ; DESCRIPTORS ; PACKAGE |
| 资助项目 | Natural Science Foundation of Zhejiang Province[LR21H300001] ; National Natural Science Foundation of China[22220102001] ; National Natural Science Foundation of China[U1909208] ; National Natural Science Foundation of China[81872798] ; Leading Talent of the Ten Thousand Plan' - National High-Level Talents Special Support Plan of China ; Fundamental Research Fund for Central Universities[2018QNA7023] ; Double Top-Class' University Project[181201*194232101] ; Key R&D Program of Zhejiang Province[2020C03010] ; West-lake Laboratory (Westlake Laboratory of Life Sciences~Sciences and Biomedicine) ; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare ; Alibaba Cloud ; Information Technology Center of Zhejiang University |
| WOS研究方向 | Biochemistry & Molecular Biology |
| 语种 | 英语 |
| 出版者 | OXFORD UNIV PRESS |
| WOS记录号 | WOS:000986726900001 |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/306611]  |
| 专题 | 新药研究国家重点实验室 |
| 通讯作者 | Zhu, Feng |
| 作者单位 | 1.East China Univ Sci & Technol, Sch Pharm, Shanghai 200237, Peoples R China 2.Zhejiang Univ, Sch Med, Affiliated Hosp 2, Coll Pharmaceut Sci, Hangzhou 310058, Peoples R China 3.Chinese Acad Sci, Shanghai Inst Mat Med, Drug Discovery & Design Ctr, State Key Lab Drug Res, Shanghai 201203, Peoples R China 4.Westlake Lab Life Sci & Biomed, Hangzhou, Zhejiang, Peoples R China 5.Zhejiang Univ, Alibaba Zhejiang Univ Joint Res Ctr Future Digital, Innovat Inst Artificial Intelligence Med, Hangzhou 330110, Peoples R China |
| 推荐引用方式 GB/T 7714 | Wang, Yunxia,Chen, Zhen,Pan, Ziqi,et al. RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction[J]. NUCLEIC ACIDS RESEARCH,2023:11. |
| APA | Wang, Yunxia.,Chen, Zhen.,Pan, Ziqi.,Huang, Shijie.,Liu, Jin.,...&Zhu, Feng.(2023).RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction.NUCLEIC ACIDS RESEARCH,11. |
| MLA | Wang, Yunxia,et al."RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction".NUCLEIC ACIDS RESEARCH (2023):11. |
入库方式： OAI收割
来源：上海药物研究所
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