Overview of Posttranslational Modifications of Biochemically Characterized Plasmodium falciparum Helicases

Chauhan, Manish; Tarique, Mohammed; Sourabh, Suman; Tuteja, Renu

doi:10.1016/b978-0-12-814685-9.00007-5

Cited by 2 publications

(1 citation statement)

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“…A wide range of PTMs have been identified so far. The common PTMs include phosphorylation, glycosylation, ubiquitination, nitrosylation, methylation, acetylation, lipidation, and proteolysis which influence almost all aspects of normal cell biology and pathogenesis 5 .…”

Section: Introductionmentioning

confidence: 99%

DeepAmp: A Convolutional Neural Network Based Tool for Predicting Protein AMPylation Sites From Binary Profile Representation

Azim

Sharma

Shatabda

et al. 2021

Preprint

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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 regulation of neurodevelopment and neurodegeneration and also involved in many physiological processes. Despite the importance of this post-translational modification, there is no peptide sequence dataset available for conducting computational 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%, and 0.55 in terms of Accuracy, Sensitivity, Specificity, and Matthews Correlation Coefficient (MCC) 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

show abstract

Section: Introductionmentioning

confidence: 99%

DeepAmp: A Convolutional Neural Network Based Tool for Predicting Protein AMPylation Sites From Binary Profile Representation

Azim

Sharma

Shatabda

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

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

Azim

Sharma

Noshadi

et al. 2022

Sci Rep

View full text Add to dashboard Cite

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.

show abstract

Overview of Posttranslational Modifications of Biochemically Characterized Plasmodium falciparum Helicases

Cited by 2 publications

References 50 publications

DeepAmp: A Convolutional Neural Network Based Tool for Predicting Protein AMPylation Sites From Binary Profile Representation

DeepAmp: A Convolutional Neural Network Based Tool for Predicting Protein AMPylation Sites From Binary Profile Representation

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

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