Attention-based convolutional neural networks for protein-protein interaction site prediction

Motivation: Protein-protein interactions are of great importance in the life cycles of living cells. Accurate prediction of the protein-protein interaction site (PPIs) from protein sequence improves our understanding of protein-protein interaction, contributes to the protein-protein docking and is crucial for drug design. However, practical experimental methods are costly and time-consuming so that many sequence-based computational methods have been developed. Most of those methods employ a sliding window approach, which utilize local neighbor information within a window size. However, they don9t distinguish and use the effect of each individual neighboring residue at different position. Results: We propose a novel sequence-based deep learning method consisting of convolutional neural networks (CNNs) and attention mechanism to improve the performance of PPIs prediction. Our attention-based CNNs captures the different effect of each neighboring residue within a sliding window, and therefore making a better understanding of the local environment of target residue. We employ experiments on several public benchmark datasets. The experimental results demonstrate that our proposed method significantly outperforms the state-of-the-art techniques. We also analyze the difference using various sliding window lengths and amino acid residue features combination. Availability and implementation: The source code can be obtained from https://github.com/biolushuai/attention-based-CNNs-for-PPIs-prediction Contact: iexfnan@zzu.edu.cn or zhangst@zzu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.