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Protein Processing, Post-Translational

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nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning.

Briefings in bioinformatics
Lysine crotonylation (Kcr) is a newly discovered type of protein post-translational modification and has been reported to be involved in various pathophysiological processes. High-resolution mass spectrometry is the primary approach for identificatio...

A comprehensive review of the imbalance classification of protein post-translational modifications.

Briefings in bioinformatics
Post-translational modifications (PTMs) play significant roles in regulating protein structure, activity and function, and they are closely involved in various pathologies. Therefore, the identification of associated PTMs is the foundation of in-dept...

Deep-Kcr: accurate detection of lysine crotonylation sites using deep learning method.

Briefings in bioinformatics
As a newly discovered protein posttranslational modification, histone lysine crotonylation (Kcr) involved in cellular regulation and human diseases. Various proteomics technologies have been developed to detect Kcr sites. However, experimental approa...

Using deep neural networks and biological subwords to detect protein S-sulfenylation sites.

Briefings in bioinformatics
Protein S-sulfenylation is one kind of crucial post-translational modifications (PTMs) in which the hydroxyl group covalently binds to the thiol of cysteine. Some recent studies have shown that this modification plays an important role in signaling t...

A machine learning-based framework for modeling transcription elongation.

Proceedings of the National Academy of Sciences of the United States of America
RNA polymerase II (Pol II) generally pauses at certain positions along gene bodies, thereby interrupting the transcription elongation process, which is often coupled with various important biological functions, such as precursor mRNA splicing and gen...

Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources.

Methods in molecular biology (Clifton, N.J.)
Most proteins undergo some form of modification after translation, and phosphorylation is one of the most relevant and ubiquitous post-translational modifications. The succession of protein phosphorylation and dephosphorylation catalyzed by protein k...

DeepSSPred: A Deep Learning Based Sulfenylation Site Predictor Via a Novel nSegmented Optimize Federated Feature Encoder.

Protein and peptide letters
BACKGROUND: S-sulfenylation (S-sulphenylation, or sulfenic acid) proteins, are special kinds of post-translation modification, which plays an important role in various physiological and pathological processes such as cytokine signaling, transcription...

DeepRMethylSite: a deep learning based approach for prediction of arginine methylation sites in proteins.

Molecular omics
Methylation, which is one of the most prominent post-translational modifications on proteins, regulates many important cellular functions. Though several model-based methylation site predictors have been reported, all existing methods employ machine ...

MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization.

Nucleic acids research
MusiteDeep is an online resource providing a deep-learning framework for protein post-translational modification (PTM) site prediction and visualization. The predictor only uses protein sequences as input and no complex features are needed, which res...

The neXtProt knowledgebase in 2020: data, tools and usability improvements.

Nucleic acids research
The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describ...