AIMC Topic: Protein Processing, Post-Translational

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Site-specific prediction of O-GlcNAc modification in proteins using evolutionary scale model.

PloS one Dec 31, 2024
Protein glycosylation, a vital post-translational modification, is pivotal in various biological processes and disease pathogenesis. Computational approaches, including protein language models and machine learning algorithms, have emerged as valuable...
Protein Processing, Post-Translational Algorithms Acetylglucosamine Evolution, Molecular Computational Biology Humans Glycoproteins Glycosylation Proteins Machine Learning Databases, Protein
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Empirical Comparison and Analysis of Artificial Intelligence-Based Methods for Identifying Phosphorylation Sites of SARS-CoV-2 Infection.

International journal of molecular sciences Dec 21, 2024
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a member of the large coronavirus family with high infectivity and pathogenicity and is the primary pathogen causing the global pandemic of coronavirus disease 2019 (COVID-19). Phosphory...
Machine Learning COVID-19 SARS-CoV-2 Humans Artificial Intelligence Protein Processing, Post-Translational Computational Biology Phosphorylation Proteome Phosphoproteins
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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...
Protein Processing, Post-Translational Proteins Amino Acid Sequence Algorithms Deep Learning Computational Biology Lysine
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Enhancing Arabidopsis thaliana ubiquitination site prediction through knowledge distillation and natural language processing.

Methods (San Diego, Calif.) Oct 22, 2024
Protein ubiquitination is a critical post-translational modification (PTM) involved in diverse biological processes and plays a pivotal role in regulating physiological mechanisms and disease states. Despite various efforts to develop ubiquitination ...
Ubiquitination Arabidopsis Proteins Arabidopsis Neural Networks, Computer Machine Learning Algorithms Computational Biology Protein Processing, Post-Translational Natural Language Processing
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Stacking based ensemble learning framework for identification of nitrotyrosine sites.

Computers in biology and medicine Oct 3, 2024
Protein nitrotyrosine is an essential post-translational modification that results from the nitration of tyrosine amino acid residues. This modification is known to be associated with the regulation and characterization of several biological function...
Humans Machine Learning Software Proteins Algorithms Databases, Protein Computational Biology Tyrosine Protein Processing, Post-Translational
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DeepPhoPred: Accurate Deep Learning Model to Predict Microbial Phosphorylation.

Proteins Sep 6, 2024
Phosphorylation is a substantial posttranslational modification of proteins that refers to adding a phosphate group to the amino acid side chain after translation process in the ribosome. It is vital to coordinate cellular functions, such as regulati...
Databases, Protein Phosphorylation Bacterial Proteins Phosphoproteins Serine Threonine Deep Learning Computational Biology Protein Processing, Post-Translational Neural Networks, Computer Software
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PSSM-Sumo: deep learning based intelligent model for prediction of sumoylation sites using discriminative features.

BMC bioinformatics Aug 30, 2024
Post-translational modifications (PTMs) are fundamental to essential biological processes, exerting significant influence over gene expression, protein localization, stability, and genome replication. Sumoylation, a PTM involving the covalent additio...
Protein Processing, Post-Translational Sumoylation Position-Specific Scoring Matrices Deep Learning Computational Biology Support Vector Machine Humans Algorithms
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Res-GCN: Identification of protein phosphorylation sites using graph convolutional network and residual network.

Computational biology and chemistry Aug 24, 2024
An essential post-translational modification, phosphorylation is intimately related with a wide range of biological activities. The advancement of effective computational methods for correctly recognizing phosphorylation sites is important for in-dep...
Humans Neural Networks, Computer Computational Biology SARS-CoV-2 Protein Processing, Post-Translational Phosphorylation
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PhosBERT: A self-supervised learning model for identifying phosphorylation sites in SARS-CoV-2-infected human cells.

Methods (San Diego, Calif.) Aug 22, 2024
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded RNA virus, which mainly causes respiratory and enteric diseases and is responsible for the outbreak of coronavirus disease 19 (COVID-19). Numerous studies have demonstr...
SARS-CoV-2 Humans Protein Processing, Post-Translational Spike Glycoprotein, Coronavirus Neural Networks, Computer Phosphorylation Computational Biology COVID-19 Supervised Machine Learning
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Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining.

Microbiome May 24, 2024
BACKGROUND: Microbial secondary metabolites play a crucial role in the intricate interactions within the natural environment. Among these metabolites, ribosomally synthesized and post-translationally modified peptides (RiPPs) are becoming a promising...
Bacteria Protein Processing, Post-Translational Microbiota Peptides Oceans and Seas Metagenomics Deep Learning Metagenome Seawater Ribosomes Bacteriophages
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