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DeepNGlypred: A deep neural network-based approach for human N-linked glycosylation site prediction
Pakhrin, Subash C. Aoki-Kinoshita, Kiyoko F. Caragea, Doina KC, Dukka B.
Pakhrin, Subash C.
Aoki-Kinoshita, Kiyoko F.
Caragea, Doina
KC, Dukka B.
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2021-12-02
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Article
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Keywords
Post-translation modification,Sequon,Deep neural network,N-linked glycosylation
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Citation
Pakhrin, S. C., Aoki-Kinoshita, K. F., Caragea, D., & Kc, D. B. (2021). DeepNgGlypred: A deep neural network-based approach for human N-linked glycosylation site prediction. Molecules, 26(23) doi:10.3390/molecules26237314
Abstract
Protein N-linked glycosylation is a post-translational modification that plays an importantrole in a myriad of biological processes. Computational prediction approaches serve as comple-mentary methods for the characterization of glycosylation sites. Most of the existing predictors forN-linked glycosylation utilize the information that the glycosylation site occurs at the N-X-[S/T] se-quon, where X is any amino acid except proline. Not all N-X-[S/T] sequons are glycosylated, thus theN-X-[S/T] sequon is a necessary but not sufficient determinant for protein glycosylation. In thatregard, computational prediction of N-linked glycosylation sites confined to N-X-[S/T] sequons is animportant problem. Here, we report DeepNGlyPred a deep learning-based approach that encodes thepositive and negative sequences in the human proteome dataset (extracted from N-GlycositeAtlas)using sequence-based features (gapped-dipeptide), predicted structural features, and evolutionaryinformation. DeepNGlyPred produces SN, SP, MCC, and ACC of 88.62%, 73.92%, 60%, and 79.41%,respectively on N-GlyDE independent test set, which is better than the compared approaches. Theseresults demonstrate that DeepNGlyPred is a robust computational technique to predict N-Linkedglycosylation sites confined to N-X-[S/T] sequon. DeepNGlyPred will be a useful resource for theglycobiology community
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This article is an open access article
distributed under the terms and
conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/).
Publisher
MDPI
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Series
Molecules;Vol. 26, Iss. 23
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1420-3049