Journal
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
Volume 19, Issue -, Pages 1512-1530Publisher
ELSEVIER
DOI: 10.1016/j.csbj.2021.03.005
Keywords
Protein-protein interactions; Protein structure; Protein function; Molecular evolution; Sequence annotation; Deep learning
Funding
- China Scholarship Council (CSC)
- DFG [FR1411/141]
Ask authors/readers for more resources
The study introduces a novel deep-learning approach for predicting interaction sites in transmembrane proteins, which outperforms existing methods. Results also show that approximately 10-25% of amino acid sites are predicted to be involved in interactions in the main functional families of human transmembrane proteins.
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 a-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. (C) 2021 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available