中国科学院机构知识库网格
Chinese Academy of Sciences Institutional Repositories Grid
首页 机构 成果 学者
  
  1. CAS IR Grid
  2. 上海药物研究所
  3. 中国科学院上海药物研究所
D3AI-Spike: A deep learning platform for predicting binding affinity between SARS-CoV-2 spike receptor binding domain with multiple amino acid mutations and human angiotensin-converting enzyme 2

文献类型：期刊论文

作者Han, Jiaxin1,2; Liu, Tingting3; Zhang, Xinben2; Yang, Yanqing2,4; Shi, Yulong2,4; Li, Jintian2,4; Ma, Minfei2,4; Zhu, Weiliang1,2,4; Gong, Likun3; Xu, Zhijian2,4
刊名COMPUTERS IN BIOLOGY AND MEDICINE
出版日期2022-12-01
卷号151页码:8
关键词D3AI-Spike ELISA Protein -protein interaction COVID-19 Deep learning
ISSN号0010-4825
DOI10.1016/j.compbiomed.2022.106212
通讯作者Zhu, Weiliang(wlzhu@simm.ac.cn) ; Gong, Likun(lkgong@cdser.simm.ac.cn) ; Xu, Zhijian(zjxu@simm.ac.cn)
英文摘要The number of SARS-CoV-2 spike Receptor Binding Domain (RBD) with multiple amino acid mutations is huge due to random mutations and combinatorial explosions, making it almost impossible to experimentally determine their binding affinities to human angiotensin-converting enzyme 2 (hACE2). Although computational prediction is an alternative way, there is still no online platform to predict the mutation effect of RBD on the hACE2 binding affinity until now. In this study, we developed a free online platform based on deep learning models, namely D3AI-Spike, for quickly predicting binding affinity between spike RBD mutants and hACE2. The models based on CNN and CNN-RNN methods have the concordance index of around 0.8. Overall, the test results of the models are in agreement with the experimental data. To further evaluate the prediction power of D3AISpike, we predicted and experimentally determined the binding affinity of a VUM (variants under monitoring) variant IHU (B.1.640.2), which has fourteen amino acid substitutions, including N501Y and E484K, and 9 deletions located in the spike protein. The predicted average affinity score for wild-type RBD and IHU to hACE2 are 0.483 and 0.438, while the determined Kaff values are 5.39 +/- 0.38 x 107 L/mol and 1.02 +/- 0.47 x 107 L/mol, respectively, demonstrating the strong predictive power of D3AI-Spike. We think D3AI-Spike will be helpful to the viral transmission prediction for the new emerging SARS-CoV-2 variants. D3AI-Spike is now available free of charge at https://www.d3pharma.com/D3Targets-2019-nCoV/D3AI-Spike/index.php.
资助项目Key project at central government level: The ability establishment of sustainable use for valuable Chinese medicine resources ; National Key R & D Program of China ; Natural Science Foundation of Shanghai ; [2060302] ; [2016YFA0502301] ; [21ZR1475600] ; [22S11902100]
WOS研究方向Life Sciences & Biomedicine - Other Topics ; Computer Science ; Engineering ; Mathematical & Computational Biology
语种英语
WOS记录号WOS:000885185300001
出版者PERGAMON-ELSEVIER SCIENCE LTD
源URL[http://119.78.100.183/handle/2S10ELR8/304662]  
专题中国科学院上海药物研究所
通讯作者Zhu, Weiliang; Gong, Likun; Xu, Zhijian
作者单位1.Nanjing Univ Chinese Med, Sch Chinese Mat Med, Nanjing 210046, Peoples R China
2.Chinese Acad Sci, Shanghai Inst Mat Med, Drug Discovery & Design Ctr, Shanghai 201203, Peoples R China
3.Chinese Acad Sci, Shanghai Inst Mat Med, Ctr Drug Safety Evaluat & Res, Shanghai 201203, Peoples R China
4.Univ Chinese Acad Sci, Sch Pharm, 19A Yuquan Rd, Beijing 100049, Peoples R China
推荐引用方式
GB/T 7714		 Han, Jiaxin,Liu, Tingting,Zhang, Xinben,et al. D3AI-Spike: A deep learning platform for predicting binding affinity between SARS-CoV-2 spike receptor binding domain with multiple amino acid mutations and human angiotensin-converting enzyme 2[J]. COMPUTERS IN BIOLOGY AND MEDICINE,2022,151:8.
APA Han, Jiaxin.,Liu, Tingting.,Zhang, Xinben.,Yang, Yanqing.,Shi, Yulong.,...&Xu, Zhijian.(2022).D3AI-Spike: A deep learning platform for predicting binding affinity between SARS-CoV-2 spike receptor binding domain with multiple amino acid mutations and human angiotensin-converting enzyme 2.COMPUTERS IN BIOLOGY AND MEDICINE,151,8.
MLA Han, Jiaxin,et al."D3AI-Spike: A deep learning platform for predicting binding affinity between SARS-CoV-2 spike receptor binding domain with multiple amino acid mutations and human angiotensin-converting enzyme 2".COMPUTERS IN BIOLOGY AND MEDICINE 151(2022):8.

入库方式： OAI收割

来源：上海药物研究所

浏览0
下载0
收藏0
其他版本

除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。