AIMC Topic: Lysine

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UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines.

BMC systems biology Jan 11, 2016
BACKGROUND: The conjugation of ubiquitin to a substrate protein (protein ubiquitylation), which involves a sequential process--E1 activation, E2 conjugation and E3 ligation, is crucial to the regulation of protein function and activity in eukaryotes....
Ubiquitination Amino Acid Motifs Sequence Analysis, Protein Datasets as Topic Lysine Machine Learning Ubiquitin Software Proteomics Proteome Mass Spectrometry Models, Molecular Protein Domains Amino Acid Sequence
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Accurate in silico identification of protein succinylation sites using an iterative semi-supervised learning technique.

Journal of theoretical biology Apr 2, 2015
As a widespread type of protein post-translational modifications (PTMs), succinylation plays an important role in regulating protein conformation, function and physicochemical properties. Compared with the labor-intensive and time-consuming experimen...
Molecular Sequence Data Protein Processing, Post-Translational Lysine Proteins Internet Artificial Intelligence Reproducibility of Results Binding Sites Amino Acids Supervised Machine Learning Algorithms Computational Biology Succinates Amino Acid Sequence Computer Simulation Support Vector Machine
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A deep learning model for prediction of lysine crotonylation sites by fusing multi-features based on multi-head self-attention mechanism.

Scientific reports May 29, 2025
Lysine crotonylation (Kcr) is an important post-translational modification, which is present in both histone and non-histone proteins, and plays a key role in a variety of biological processes such as metabolism and cell differentiation. Therefore, r...
Protein Processing, Post-Translational Natural Language Processing Lysine Humans Histones Neural Networks, Computer Deep Learning
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MlyPredCSED: based on extreme point deviation compensated clustering combined with cross-scale convolutional neural networks to predict multiple lysine sites in human.

Briefings in bioinformatics Mar 4, 2025
In post-translational modification, covalent bonds on lysine and attached chemical groups significantly change proteins' physical and chemical properties. They shape protein structures, enhance function and stability, and are vital for physiological ...
Protein Processing, Post-Translational Proteins Lysine Convolutional Neural Networks Computational Biology Cluster Analysis Humans Neural Networks, Computer Software Algorithms
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Lactylation prediction models based on protein sequence and structural feature fusion.

Briefings in bioinformatics Jan 22, 2024
Lysine lactylation (Kla) is a newly discovered posttranslational modification that is involved in important life activities, such as glycolysis-related cell function, macrophage polarization and nervous system regulation, and has received widespread ...
Protein Processing, Post-Translational Natural Language Processing Protein Domains Amino Acid Sequence Lysine
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Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences.

Database : the journal of biological databases and curation Jan 19, 2024
The post-translational modifications occur as crucial molecular regulatory mechanisms utilized to regulate diverse cellular processes. Malonylation of proteins, a reversible post-translational modification of lysine/k residues, is linked to a variety...
Proteins Lysine Machine Learning Deep Learning Protein Processing, Post-Translational
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PLP_FS: prediction of lysine phosphoglycerylation sites in protein using support vector machine and fusion of multiple F_Score feature selection.

Briefings in bioinformatics Sep 20, 2022
A newly invented post-translational modification (PTM), phosphoglycerylation, has shown its essential role in the construction and functional properties of proteins and dangerous human diseases. Hence, it is very urgent to know about the molecular me...
Lysine Protein Processing, Post-Translational Proteins Amino Acid Sequence Algorithms Computational Biology Support Vector Machine Humans
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DeepHisCoM: deep learning pathway analysis using hierarchical structural component models.

Briefings in bioinformatics Sep 20, 2022
Many statistical methods for pathway analysis have been used to identify pathways associated with the disease along with biological factors such as genes and proteins. However, most pathway analysis methods neglect the complex nonlinear relationship ...
Isoleucine Leucine Valine Mitogen-Activated Protein Kinases Gonadotropin-Releasing Hormone Tryptophan Biological Factors Phenylalanine Lysine Tyrosine Humans Deep Learning COVID-19 Liver Neoplasms Carcinoma, Hepatocellular
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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...
Neural Networks, Computer ROC Curve Computational Biology Protein Processing, Post-Translational Reproducibility of Results Phosphorylation Software Deep Learning Lysine Algorithms User-Computer Interface Databases, Factual
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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...
Machine Learning Language Protein Processing, Post-Translational Natural Language Processing Lysine
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