Drug-target binding affinity prediction method based on a deep graph neural network

Dong Ma; Shuang Li; Zhihua Chen; Dong Ma; Shuang Li; Zhihua Chen

doi:10.3934/mbe.2023012

Mathematical Biosciences and Engineering

2023, Volume 20, Issue 1: 269-282. doi: 10.3934/mbe.2023012

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Drug-target binding affinity prediction method based on a deep graph neural network

1.
Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
2.
Beidahuang Industry Group General Hospital, Harbin, China

Academic Editor: Leyi Wei
† The authors contributed equally to this work.

Received: 01 August 2022 Revised: 06 September 2022 Accepted: 07 September 2022 Published: 30 September 2022

The development of new drugs is a long and costly process, Computer-aided drug design reduces development costs while computationally shortening the new drug development cycle, in which DTA (Drug-Target binding Affinity) prediction is a key step to screen out potential drugs. With the development of deep learning, various types of deep learning models have achieved notable performance in a wide range of fields. Most current related studies focus on extracting the sequence features of molecules while ignoring the valuable structural information; they employ sequence data that represent only the elemental composition of molecules without considering the molecular structure maps that contain structural information. In this paper, we use graph neural networks to predict DTA based on corresponding graph data of drugs and proteins, and we achieve competitive performance on two benchmark datasets, Davis and KIBA. In particular, an MSE of 0.227 and CI of 0.895 were obtained on Davis, and an MSE of 0.127 and CI of 0.903 were obtained on KIBA.
- artificial intelligence,
- biological sequence analysis,
- deep learning,
- binding affinity prediction,
- graph convolution network
Citation: Dong Ma, Shuang Li, Zhihua Chen. Drug-target binding affinity prediction method based on a deep graph neural network[J]. Mathematical Biosciences and Engineering, 2023, 20(1): 269-282. doi: 10.3934/mbe.2023012

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Abstract

The development of new drugs is a long and costly process, Computer-aided drug design reduces development costs while computationally shortening the new drug development cycle, in which DTA (Drug-Target binding Affinity) prediction is a key step to screen out potential drugs. With the development of deep learning, various types of deep learning models have achieved notable performance in a wide range of fields. Most current related studies focus on extracting the sequence features of molecules while ignoring the valuable structural information; they employ sequence data that represent only the elemental composition of molecules without considering the molecular structure maps that contain structural information. In this paper, we use graph neural networks to predict DTA based on corresponding graph data of drugs and proteins, and we achieve competitive performance on two benchmark datasets, Davis and KIBA. In particular, an MSE of 0.227 and CI of 0.895 were obtained on Davis, and an MSE of 0.127 and CI of 0.903 were obtained on KIBA.

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