AIMC Topic: Protein Processing, Post-Translational

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

Briefings in bioinformatics Jul 20, 2021
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...
Humans Deep Learning Sequence Analysis, Protein Acylation Crotonates Protein Processing, Post-Translational Databases, Protein Lysine
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Using deep neural networks and biological subwords to detect protein S-sulfenylation sites.

Briefings in bioinformatics May 20, 2021
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...
Sulfenic Acids Databases, Protein Sequence Analysis, Protein Neural Networks, Computer Protein Processing, Post-Translational
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A machine learning-based framework for modeling transcription elongation.

Proceedings of the National Academy of Sciences of the United States of America Feb 9, 2021
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...
Humans Machine Learning Models, Biological HeLa Cells HEK293 Cells Epigenesis, Genetic DNA Methylation Protein Processing, Post-Translational Nucleotide Motifs RNA Splicing RNA Splice Sites Transcription Elongation, Genetic Histones Base Sequence Binding Sites Genome, Human RNA Polymerase II
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Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2021
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...
Substrate Specificity Phosphoric Monoester Hydrolases Protein Processing, Post-Translational Phosphorylation Protein Kinases Neural Networks, Computer Proteome
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DeepSSPred: A Deep Learning Based Sulfenylation Site Predictor Via a Novel nSegmented Optimize Federated Feature Encoder.

Protein and peptide letters Jan 1, 2021
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...
Sulfenic Acids Proteins Databases, Protein Machine Learning Deep Learning Computational Biology Protein Processing, Post-Translational
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DeepRMethylSite: a deep learning based approach for prediction of arginine methylation sites in proteins.

Molecular omics Oct 12, 2020
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 ...
ROC Curve Protein Processing, Post-Translational Proteins Databases, Protein Methylation Arginine Algorithms Neural Networks, Computer Reproducibility of Results Deep Learning
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MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization.

Nucleic acids research Jul 2, 2020
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...
Protein Processing, Post-Translational Proteins Models, Molecular Internet Protein Conformation Computer Graphics Software Deep Learning Sequence Analysis, Protein
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The neXtProt knowledgebase in 2020: data, tools and usability improvements.

Nucleic acids research Jan 8, 2020
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...
Trypsin Protein Kinases Knowledge Bases Software Proteins Sequence Analysis, RNA Humans Peptides Databases, Protein User-Computer Interface Mass Spectrometry Internet Protein Processing, Post-Translational
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Prediction of S-nitrosylation sites by integrating support vector machines and random forest.

Molecular omics Dec 2, 2019
Cysteine S-nitrosylation is a type of reversible post-translational modification of proteins, which controls diverse biological processes. It is associated with redox-based cellular signaling to protect against oxidative stress. The identification of...
Software Algorithms Computational Biology Cysteine Support Vector Machine Protein Processing, Post-Translational
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Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.

Briefings in bioinformatics Nov 27, 2019
Lysine post-translational modifications (PTMs) play a crucial role in regulating diverse functions and biological processes of proteins. However, because of the large volumes of sequencing data generated from genome-sequencing projects, systematic id...
Lysine Computational Biology Protein Processing, Post-Translational Feasibility Studies Machine Learning Algorithms
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