A convolutional neural network based tool for predicting protein AMPylation sites from binary profile representation

Sayed Mehedi Azim, Alok Sharma, Iman Noshadi, Swakkhar Shatabda, Iman Dehzangi

Research output: Contribution to journalArticlepeer-review

Abstract

AMPylation is an emerging post-translational modification that occurs on the hydroxyl group of threonine, serine, or tyrosine via a phosphodiester bond. AMPylators catalyze this process as covalent attachment of adenosine monophosphate to the amino acid side chain of a peptide. Recent studies have shown that this post-translational modification is directly responsible for the regulation of neurodevelopment and neurodegeneration and is also involved in many physiological processes. Despite the importance of this post-translational modification, there is no peptide sequence dataset available for conducting computation analysis. Therefore, so far, no computational approach has been proposed for predicting AMPylation. In this study, we introduce a new dataset of this distinct post-translational modification and develop a new machine learning tool using a deep convolutional neural network called DeepAmp to predict AMPylation sites in proteins. DeepAmp achieves 77.7%, 79.1%, 76.8%, 0.55, and 0.85 in terms of Accuracy, Sensitivity, Specificity, Matthews Correlation Coefficient, and Area Under Curve for AMPylation site prediction task, respectively. As the first machine learning model, DeepAmp demonstrate promising results which highlight its potential to solve this problem. Our presented dataset and DeepAmp as a standalone predictor are publicly available at https://github.com/MehediAzim/DeepAmp.

Original languageEnglish (US)
Article number11451
JournalScientific Reports
Volume12
Issue number1
DOIs
StatePublished - Dec 2022
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General

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