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- Publisher Website: 10.1038/s41467-022-34807-3
- Scopus: eid_2-s2.0-85142392342
- PMID: 36414666
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Article: DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs
Title | DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs |
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Authors | |
Issue Date | 2022 |
Citation | Nature Communications, 2022, v. 13, n. 1, article no. 7133 How to Cite? |
Abstract | The rational design of PROTACs is difficult due to their obscure structure-activity relationship. This study introduces a deep neural network model - DeepPROTACs to help design potent PROTACs molecules. It can predict the degradation capacity of a proposed PROTAC molecule based on structures of given target protein and E3 ligase. The experimental dataset is mainly collected from PROTAC-DB and appropriately labeled according to the DC50 and Dmax values. In the model of DeepPROTACs, the ligands as well as the ligand binding pockets are generated and represented with graphs and fed into Graph Convolutional Networks for feature extraction. While SMILES representations of linkers are fed into a Bidirectional Long Short-Term Memory layer to generate the features. Experiments show that DeepPROTACs model achieves 77.95% average prediction accuracy and 0.8470 area under receiver operating characteristic curve on the test set. DeepPROTACs is available online at a web server (https://bailab.siais.shanghaitech.edu.cn/services/deepprotacs/) and at github (https://github.com/fenglei104/DeepPROTACs). |
Persistent Identifier | http://hdl.handle.net/10722/345289 |
DC Field | Value | Language |
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dc.contributor.author | Li, Fenglei | - |
dc.contributor.author | Hu, Qiaoyu | - |
dc.contributor.author | Zhang, Xianglei | - |
dc.contributor.author | Sun, Renhong | - |
dc.contributor.author | Liu, Zhuanghua | - |
dc.contributor.author | Wu, Sanan | - |
dc.contributor.author | Tian, Siyuan | - |
dc.contributor.author | Ma, Xinyue | - |
dc.contributor.author | Dai, Zhizhuo | - |
dc.contributor.author | Yang, Xiaobao | - |
dc.contributor.author | Gao, Shenghua | - |
dc.contributor.author | Bai, Fang | - |
dc.date.accessioned | 2024-08-15T09:26:24Z | - |
dc.date.available | 2024-08-15T09:26:24Z | - |
dc.date.issued | 2022 | - |
dc.identifier.citation | Nature Communications, 2022, v. 13, n. 1, article no. 7133 | - |
dc.identifier.uri | http://hdl.handle.net/10722/345289 | - |
dc.description.abstract | The rational design of PROTACs is difficult due to their obscure structure-activity relationship. This study introduces a deep neural network model - DeepPROTACs to help design potent PROTACs molecules. It can predict the degradation capacity of a proposed PROTAC molecule based on structures of given target protein and E3 ligase. The experimental dataset is mainly collected from PROTAC-DB and appropriately labeled according to the DC50 and Dmax values. In the model of DeepPROTACs, the ligands as well as the ligand binding pockets are generated and represented with graphs and fed into Graph Convolutional Networks for feature extraction. While SMILES representations of linkers are fed into a Bidirectional Long Short-Term Memory layer to generate the features. Experiments show that DeepPROTACs model achieves 77.95% average prediction accuracy and 0.8470 area under receiver operating characteristic curve on the test set. DeepPROTACs is available online at a web server (https://bailab.siais.shanghaitech.edu.cn/services/deepprotacs/) and at github (https://github.com/fenglei104/DeepPROTACs). | - |
dc.language | eng | - |
dc.relation.ispartof | Nature Communications | - |
dc.title | DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs | - |
dc.type | Article | - |
dc.description.nature | link_to_subscribed_fulltext | - |
dc.identifier.doi | 10.1038/s41467-022-34807-3 | - |
dc.identifier.pmid | 36414666 | - |
dc.identifier.scopus | eid_2-s2.0-85142392342 | - |
dc.identifier.volume | 13 | - |
dc.identifier.issue | 1 | - |
dc.identifier.spage | article no. 7133 | - |
dc.identifier.epage | article no. 7133 | - |
dc.identifier.eissn | 2041-1723 | - |