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Luo Y, Liu L, He Z, Zhang S, Huo P, Wang Z, Jiaxin Q, Zhao L, Wu Y, Zhang D, Bu D, Chen R, Zhao Y. Corrigendum to "TREAT: Therapeutic RNAs exploration inspired by artificial intelligence technology" [Comput Struct Biotechnol J 20 (2022) 5680-5689]. Comput Struct Biotechnol J 2023; 21:3540. [PMID: 37484489 PMCID: PMC10362727 DOI: 10.1016/j.csbj.2023.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
[This corrects the article DOI: 10.1016/j.scr.2023.103115.].
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Affiliation(s)
- Yufan Luo
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liu Liu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Zihao He
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Shanshan Zhang
- Luoyang Zhongke Information Industry Research Institute, Luoyang, China
| | - Peipei Huo
- Luoyang Zhongke Information Industry Research Institute, Luoyang, China
| | - Zhihao Wang
- Luoyang Zhongke Information Industry Research Institute, Luoyang, China
| | - Qin Jiaxin
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lianhe Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Yang Wu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Dongdong Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dechao Bu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- Hwa Mei Hospital, University of Chinese Academy of Sciences, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Shenzhen Institute of Nucleic Acid Drug Research, Shenzhen Bay Laboratory Pingshan Translational Medicine Center, Shenzhen 510800, China
| | - Yi Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
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Luo Y, Liu L, He Z, Zhang S, Huo P, Wang Z, Jiaxin Q, Zhao L, Wu Y, Zhang D, Bu D, Chen R, Zhao Y. TREAT: Therapeutic RNAs exploration inspired by artificial intelligence technology. Comput Struct Biotechnol J 2022; 20:5680-5689. [PMID: 36320935 PMCID: PMC9589171 DOI: 10.1016/j.csbj.2022.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/08/2022] Open
Abstract
Recent advances in RNA engineering have enabled the development of RNA-based therapeutics for a broad spectrum of applications. Developing RNA therapeutics start with targeted RNA screening and move to the drug design and optimization. However, existing target screening tools ignore noncoding RNAs and their disease-relevant regulatory relationships. And designing therapeutic RNAs encounters high computational complexity of multi-objective optimization to overcome the immunogenicity, instability and inefficient translational production. To unlock the therapeutic potential of noncoding RNAs and enable one-stop screening and design of therapeutic RNAs, we have built the platform TREAT. It incorporates 43,087,953 regulatory relationships between coding and noncoding genes from 81 biological networks under different physiological conditions. TREAT introduces graph representation learning with Random Walk Diffusions to perform disease-relevant target screening, in addition to the commonly utilized Topological Degree and PageRank algorithms. Design and optimization of large RNAs or interfering RNAs are both available. To reduce the computational complexity of multi-objective optimization for large RNA, we stratified the features into local and global features. The local features are evaluated on the fixed-length or dynamic-length local bins, whereas the latter are inspired by AI language models of protein sequence. Then the global assessment is performed on refined candidates, thus reducing the enormous search space. Overall, TREAT is a one-stop platform for the screening and designing of therapeutic RNAs, with particular attention to noncoding RNAs and cutting-edge AI technology embedded, leading the progress of innovative therapeutics for challenging diseases. TREAT is freely accessible at https://rna.org.cn/treat.
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Affiliation(s)
- Yufan Luo
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liu Liu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Zihao He
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Shanshan Zhang
- Luoyang Zhongke Information Industry Research Institute, Luoyang, China
| | - Peipei Huo
- Luoyang Zhongke Information Industry Research Institute, Luoyang, China
| | - Zhihao Wang
- Luoyang Zhongke Information Industry Research Institute, Luoyang, China
| | - Qin Jiaxin
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lianhe Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Yang Wu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Dongdong Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dechao Bu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China,Hwa Mei Hospital, University of Chinese Academy of Sciences, China,Correspondence authors at: Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China (Y. Zhao).
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China,Shenzhen Institute of Nucleic Acid Drug Research, Shenzhen Bay Laboratory Pingshan Translational Medicine Center, Shenzhen 510800, China,Correspondence authors at: Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China (Y. Zhao).
| | - Yi Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China,Correspondence authors at: Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China (Y. Zhao).
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