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GlyNet: A Multi-Task Neural Network for Predicting Protein-Glycan Interactions

Eric J. Carpenter, Shaurya Seth, Noel Yue, Russell Greiner, Ratmir Derda
doi: https://doi.org/10.1101/2021.05.28.446094
Eric J. Carpenter
1Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Shaurya Seth
1Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Noel Yue
1Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Russell Greiner
2Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
3Alberta Machine Intelligence Institute (AMII), Edmonton, Alberta, Canada
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Ratmir Derda
1Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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  • For correspondence: ratmir@ualberta.ca
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Abstract

Advances in diagnostics, therapeutics, vaccines, transfusion, and organ transplantation build on a fundamental understanding of glycan-protein interactions. To aid this, we developed GlyNet, a model that accurately predicts interactions (relative binding strengths) between mammalian glycans and 352 glycan-binding proteins, many at multiple concentrations. For each glycan input, our model produces 1257 outputs, each representing the relative interaction strength between the input glycan and a particular protein sample. GlyNet learns these continuous values using relative fluorescence units (RFUs) measured on 599 glycans in the Consortium for Functional Glycomics glycan arrays and extrapolates these to RFUs from additional, untested glycans. GlyNet’s output of continuous values provides more detailed results than classification models. Such continuous outputs are easily converted by a following classifier, and in this form GlyNet outperforms reported classifiers. GlyNet is the first multi-output regression model for protein-glycan interactions and will serve as an important benchmark, facilitating development of quantitative computational glycobiology.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 30, 2021.
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GlyNet: A Multi-Task Neural Network for Predicting Protein-Glycan Interactions
Eric J. Carpenter, Shaurya Seth, Noel Yue, Russell Greiner, Ratmir Derda
bioRxiv 2021.05.28.446094; doi: https://doi.org/10.1101/2021.05.28.446094
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GlyNet: A Multi-Task Neural Network for Predicting Protein-Glycan Interactions
Eric J. Carpenter, Shaurya Seth, Noel Yue, Russell Greiner, Ratmir Derda
bioRxiv 2021.05.28.446094; doi: https://doi.org/10.1101/2021.05.28.446094

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