FMCA-DTI: A Fragment-oriented method based on a Multihead Cross Attention mechanism to improve Drug-Target Interaction prediction.

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Abstract

Identifying drug-target interactions (DTI) is crucial in drug discovery. Fragments are less complex and can accurately characterize local features, which is important in DTI prediction. Recently, deep learning (DL) -based methods predict DTI more efficiently. However, two challenges remain in existing DL-based methods: (i) some methods directly encode drugs and proteins into integers, ignoring the substructure representation; (ii) some methods learn the features of the drugs and proteins separately instead of considering their interactions.In this paper, we propose a fragment-oriented method based on a multihead cross attention mechanism for predicting DTI, named FMCA-DTI. FMCA-DTI obtains multiple types of fragments of drugs and proteins by branch chain mining and category fragment mining. Importantly, FMCA-DTI utilizes the shared-weight-based multihead cross attention mechanism to learn the complex interaction features between different fragments. Experiments on three benchmark datasets show that FMCA-DTI achieves significantly improved performance by comparing it with four state-of-the-art baselines.The code for this workflow is available at: https://github.com/jacky102022/FMCA-DTI.Supplementary data are available at Bioinformatics online.© The Author(s) 2024. Published by Oxford University Press.