AIMC Topic: Lysine

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Machine learning-guided evolution of pyrrolysyl-tRNA synthetase for improved incorporation efficiency of diverse noncanonical amino acids.

Nature communications Jul 19, 2025
The pyrrolysyl-tRNA synthetase (PylRS) is widely used to incorporate noncanonical amino acids (ncAAs) into proteins. However, the yields of most ncAA-containing protein  remain low due to the limited activity of PylRS variants. Here, we apply machine...
Lysine Directed Molecular Evolution Protein Engineering Amino Acids RNA, Transfer Amino Acyl-tRNA Synthetases Machine Learning Codon, Terminator Mutation
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EUP: Enhanced cross-species prediction of ubiquitination sites via a conditional variational autoencoder network based on ESM2.

PLoS computational biology Jul 16, 2025
Ubiquitination is critical in biomedical research. Predicting ubiquitination sites based on deep learning model have advanced the study of ubiquitination. However, traditional supervised model limits in the scenarios where labels are scarcity across ...
Humans Lysine Autoencoder Ubiquitination Deep Learning Computational Biology Species Specificity Software Animals
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Comprehensive analysis of scRNA-seq and bulk RNA-seq data via machine learning and bioinformatics reveals the role of lysine metabolism-related genes in gastric carcinogenesis.

BMC cancer Apr 9, 2025
BACKGROUND: Gastric cancer (GC) is a highly aggressive and heterogeneous cancer with extremely complex biological characteristics. Lysine and its metabolism are closely related to human cancer, but little is known about how lysine metabolism-related ...
Computational Biology Sequence Analysis, RNA Gene Expression Regulation, Neoplastic Gene Regulatory Networks Single-Cell Gene Expression Analysis Vimentin Lysine Cell Proliferation Carcinogenesis Nomograms Stomach Neoplasms Biomarkers, Tumor Single-Cell Analysis RNA-Seq Cell Line, Tumor Humans Machine Learning Prognosis
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SSE-Net: A novel network based on sequence spatial equation for Camellia sinensis lysine acetylation identification.

Computational biology and chemistry Mar 28, 2025
Lysine acetylation (Kace) is one of the most important post-translational modifications. It is key to identify Kace sites for understanding regulation mechanisms in Camellia sinensis. In this study, we defined a mathematical formula, named sequence s...
Camellia sinensis Acetylation Lysine Protein Processing, Post-Translational
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Lipid discovery enabled by sequence statistics and machine learning.

eLife Dec 10, 2024
Bacterial membranes are complex and dynamic, arising from an array of evolutionary pressures. One enzyme that alters membrane compositions through covalent lipid modification is MprF. We recently identified that MprF synthesizes lysyl-phosphatidylgl...
Machine Learning Bacterial Proteins Substrate Specificity Lysine Enterococcus Phosphatidylglycerols Streptococcus agalactiae Glycolipids
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Machine Learning Guided Rational Design of a Non-Heme Iron-Based Lysine Dioxygenase Improves its Total Turnover Number.

Chembiochem : a European journal of chemical biology Dec 5, 2024
Highly selective C-H functionalization remains an ongoing challenge in organic synthetic methodologies. Biocatalysts are robust tools for achieving these difficult chemical transformations. Biocatalyst engineering has often required directed evolutio...
Protein Engineering Dioxygenases Machine Learning Iron Molecular Dynamics Simulation Mutation Lysine
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DeepKlapred: A deep learning framework for identifying protein lysine lactylation sites via multi-view feature fusion.

International journal of biological macromolecules Nov 19, 2024
Lysine lactylation (Kla) is a post-translational modification (PTM) that holds significant importance in the regulation of various biological processes. While traditional experimental methods are highly accurate for identifying Kla sites, they are bo...
Lysine Deep Learning Proteins Algorithms Computational Biology Amino Acid Sequence Protein Processing, Post-Translational
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iBhb-Lys: Identify lysine β-hydroxybutyrylation sites using autoencoder feature representation and fuzzy SVM algorithm.

Analytical biochemistry Nov 7, 2024
Lysine β-hydroxybutyrylation (Kbhb) is newly discovered β-hydroxybutyrylate-derived histone modification which has been associated with the pathogenesis of many human diseases. To further elucidate the biological significance and molecular mechanism ...
Support Vector Machine Fuzzy Logic Lysine Humans Algorithms
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KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites.

Methods (San Diego, Calif.) Apr 27, 2024
Lysine β-hydroxybutyrylation is an important post-translational modification (PTM) involved in various physiological and biological processes. In this research, we introduce a novel predictor KbhbXG, which utilizes XGBoost to identify β-hydroxybutyry...
Proteomics Software Protein Processing, Post-Translational Algorithms Lysine Computational Biology Humans Machine Learning
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Predicting lysine methylation sites using a convolutional neural network.

Methods (San Diego, Calif.) Apr 9, 2024
Protein lysine methylation is a particular type of post translational modification that plays an important role in both histone and non-histone function regulation in proteins. Deregulation caused by lysine methyltransferases has been identified as t...
Protein Processing, Post-Translational Methylation Lysine Humans Histone-Lysine N-Methyltransferase Neural Networks, Computer Machine Learning Computational Biology
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