AIMC Topic: Protein Processing, Post-Translational

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Adapt-Kcr: a novel deep learning framework for accurate prediction of lysine crotonylation sites based on learning embedding features and attention architecture.

Briefings in bioinformatics Mar 10, 2022
Protein lysine crotonylation (Kcr) is an important type of posttranslational modification that is associated with a wide range of biological processes. The identification of Kcr sites is critical to better understanding their functional mechanisms. H...
Deep Learning User-Computer Interface Databases, Factual Reproducibility of Results Protein Processing, Post-Translational Phosphorylation Lysine ROC Curve Computational Biology Software Algorithms Neural Networks, Computer
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BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models.

Bioinformatics (Oxford, England) Jan 12, 2022
MOTIVATION: As one of the most important post-translational modifications (PTMs), protein lysine crotonylation (Kcr) has attracted wide attention, which involves in important physiological activities, such as cell differentiation and metabolism. Howe...
Natural Language Processing Language Machine Learning Lysine Protein Processing, Post-Translational
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Deep Learning-Based Advances In Protein Posttranslational Modification Site and Protein Cleavage Prediction.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2022
Posttranslational modification (PTM ) is a ubiquitous phenomenon in both eukaryotes and prokaryotes which gives rise to enormous proteomic diversity. PTM mostly comes in two flavors: covalent modification to polypeptide chain and proteolytic cleavage...
Protein Processing, Post-Translational Proteins Proteomics Mass Spectrometry Deep Learning
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Enhancing the Discovery of Functional Post-Translational Modification Sites with Machine Learning Models - Development, Validation, and Interpretation.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2022
Protein posttranslational modifications (PTMs) are a rapidly expanding feature class of significant importance in cell biology. Due to a high burden of experimental proof, the number of functionals PTMs in the eukaryotic proteome is currently underes...
Protein Processing, Post-Translational Machine Learning Proteome Neural Networks, Computer
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Computational Prediction of N- and O-Linked Glycosylation Sites for Human and Mouse Proteins.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2022
Protein glycosylation is one of the most complex posttranslational modifications (PTM) that play a fundamental role in protein function. Identification and annotation of these sites using experimental approaches are challenging and time consuming. He...
Animals Mice Humans Support Vector Machine Protein Processing, Post-Translational Proteins Computational Biology Glycosylation Amino Acid Sequence
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PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein-protein interaction information.

Bioinformatics (Oxford, England) Dec 11, 2021
MOTIVATION: Phosphorylation is one of the most studied post-translational modifications, which plays a pivotal role in various cellular processes. Recently, deep learning methods have achieved great success in prediction of phosphorylation sites, but...
Amino Acid Sequence Neural Networks, Computer Proteins Phosphorylation 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 Nov 5, 2021
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...
Software Deep Learning Humans Sequence Analysis, Protein Databases, Protein Computational Biology Histones Protein Processing, Post-Translational
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A comprehensive review of the imbalance classification of protein post-translational modifications.

Briefings in bioinformatics Sep 2, 2021
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...
Databases, Protein Models, Biological Protein Processing, Post-Translational Proteins Reproducibility of Results Computational Biology Neural Networks, Computer Machine Learning Humans Algorithms
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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...
Sequence Analysis, Protein Acylation Databases, Protein Lysine Humans Crotonates Deep Learning Protein Processing, Post-Translational
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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...
Neural Networks, Computer Sulfenic Acids Databases, Protein Protein Processing, Post-Translational Sequence Analysis, Protein
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