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标题：Improved sequence-based prediction of interaction sites in α-helical transmembrane proteins by deep learning
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作者：Jianfeng Sun ; Dmitrij Frishman
期刊名称：Computational and Structural Biotechnology Journal
印刷版ISSN：2001-0370
出版年度：2021
卷号：19
页码：1512-1530
DOI：10.1016/j.csbj.2021.03.005
出版社：Computational and Structural Biotechnology Journal
摘要：Interactions between transmembrane (TM) proteins are fundamental for a wide spectrum of cellular functions, but precise molecular details of these interactions remain largely unknown due to the scarcity of experimentally determined three-dimensional complex structures. Computational techniques are therefore required for a large-scale annotation of interaction sites in TM proteins. Here, we present a novel deep-learning approach, DeepTMInter, for sequence-based prediction of interaction sites in α-helical TM proteins based on their topological, physiochemical, and evolutionary properties. Using a combination of ultra-deep residual neural networks with a stacked generalization ensemble technique DeepTMInter significantly outperforms existing methods, achieving the AUC/AUCPR values of 0.689/0.598. Across the main functional families of human transmembrane proteins, the percentage of amino acid sites predicted to be involved in interactions typically ranges between 10% and 25%, and up to 30% in ion channels. DeepTMInter is available as a standalone package at https://github.com/2003100127/deeptminter . The training and benchmarking datasets are available at https://data.mendeley.com/datasets/2t8kgwzp35 .
关键词：Protein-protein interactions ; Protein structure ; Protein function ; Molecular evolution ; Sequence annotation ; Deep learning