Journal
BRIEFINGS IN BIOINFORMATICS
Volume 22, Issue 5, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbab117
Keywords
deep learning; drug-target interaction; self-attention; COVID-19
Funding
- National Natural Science Foundation of China [61971296, U19A2078]
- Sichuan Science and Technology Planning Project [2020YFG0319, 2020YFH0186]
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In this study, an end-to-end model with multiple attention blocks was proposed to predict the binding affinity scores of drug-target pairs. The model encodes correlations between atoms using a relation-aware self-attention block and models the interaction between drug and target representations using a multi-head attention block. Experimental results show that the proposed approach outperforms existing methods by benefiting from encoded correlation and extracted interaction information.
Drug-target interaction (DTI) prediction has drawn increasing interest due to its substantial position in the drug discovery process. Many studies have introduced computational models to treat DTI prediction as a regression task, which directly predict the binding affinity of drug-target pairs. However, existing studies (i) ignore the essential correlations between atoms when encoding drug compounds and (ii) model the interaction of drug-target pairs simply by concatenation. Based on those observations, in this study, we propose an end-to-end model with multiple attention blocks to predict the binding affinity scores of drug-target pairs. Our proposed model offers the abilities to (i) encode the correlations between atoms by a relation-aware self-attention block and (ii) model the interaction of drug representations and target representations by the multi-head attention block. Experimental results of DTI prediction on two benchmark datasets show our approach outperforms existing methods, which are benefit from the correlation information encoded by the relation-aware self-attention block and the interaction information extracted by the multi-head attention block. Moreover, we conduct the experiments on the effects of max relative position length and find out the best max relative position length value . Furthermore, we apply our model to predict the binding affinity of Corona Virus Disease 2019 (COVID-19)-related genome sequences and FDA-approved drugs.
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