AIMC Topic: Proteolysis

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Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence.

Journal of the American Chemical Society Jan 27, 2023
Only around 20% of the human proteome is considered to be druggable with small-molecule antagonists. This leaves some of the most compelling therapeutic targets outside the reach of ligand discovery. The concept of targeted protein degradation (TPD) ...
Humans Ubiquitin-Protein Ligases Proteolysis Ubiquitination Artificial Intelligence Multiomics
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Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation.

Genomics, proteomics & bioinformatics Dec 6, 2022
Targeted protein degradation (TPD) has rapidly emerged as a therapeutic modality to eliminate previously undruggable proteins by repurposing the cell's endogenous protein degradation machinery. However, the susceptibility of proteins for targeting by...
Proteolysis Ubiquitination Proteome Lysine Machine Learning
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Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning.

BMC biology Jul 14, 2022
BACKGROUND: Degrons are short linear motifs, bound by E3 ubiquitin ligase to target protein substrates to be degraded by the ubiquitin-proteasome system. Mutations leading to deregulation of degron functionality disrupt control of protein abundance d...
Proteome Deep Learning Ubiquitin Ubiquitin-Protein Ligases Proteolysis
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Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides.

Analytical chemistry May 12, 2022
The prediction of fragment ion intensities and retention time of peptides has gained significant attention over the past few years. However, the progress shown in the accurate prediction of such properties focused primarily on unlabeled peptides. Tan...
Infant, Newborn Peptides Deep Learning Humans Proteolysis Proteomics Tandem Mass Spectrometry
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Machine Learning Approaches for Metalloproteins.

Molecules (Basel, Switzerland) Feb 14, 2022
Metalloproteins are a family of proteins characterized by metal ion binding, whereby the presence of these ions confers key catalytic and ligand-binding properties. Due to their ubiquity among biological systems, researchers have made immense efforts...
Proteolysis Binding Sites Amino Acid Sequence Protein Stability Metalloproteins Machine Learning Drug Design Structure-Activity Relationship Models, Molecular Protein Binding
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DeepDigest: Prediction of Protein Proteolytic Digestion with Deep Learning.

Analytical chemistry Apr 7, 2021
Proteolytic digestion of proteins by one or more proteases is a key step in shotgun proteomics, in which the proteolytic products, i.e., peptides, are taken as the surrogates of their parent proteins for further qualitative or quantitative analysis. ...
Proteolysis Peptide Hydrolases Deep Learning Proteomics
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Predicting Proteolysis in Complex Proteomes Using Deep Learning.

International journal of molecular sciences Mar 17, 2021
Both protease- and reactive oxygen species (ROS)-mediated proteolysis are thought to be key effectors of tissue remodeling. We have previously shown that comparison of amino acid composition can predict the differential susceptibilities of proteins t...
Humans Neural Networks, Computer Amino Acids Ultraviolet Rays Peptide Hydrolases Software Deep Learning Proteome Extracellular Matrix Proteins Reproducibility of Results Proteolysis Reactive Oxygen Species
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Systematic characterization of mutations altering protein degradation in human cancers.

Molecular cell Feb 9, 2021
The ubiquitin-proteasome system (UPS) is the primary route for selective protein degradation in human cells. The UPS is an attractive target for novel cancer therapies, but the precise UPS genes and substrates important for cancer growth are incomple...
Humans Mutation Neoplasms HEK293 Cells Proteolysis Models, Genetic Neoplasm Proteins Deep Learning Cell Line, Tumor
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Application of artificial neural networks to predict multiple quality of dry-cured ham based on protein degradation.

Food chemistry Nov 9, 2020
This study investigated protein degradation and quality changes during the processing of dry-cured ham, and then established the multiple quality prediction model based on protein degradation. From the raw material to the curing period, proteolysis i...
Amino Acids Proteolysis Swine Color Neural Networks, Computer Pork Meat Desiccation Animals Chromatography, Ion Exchange
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Discovery of gene module acting on ubiquitin-mediated proteolysis pathway by co-expression network analysis for endometriosis.

Reproductive biomedicine online Oct 14, 2020
RESEARCH QUESTION: Is abnormal gene module expression in the eutopic endometrium related to the occurrence of endometriosis?
Endometriosis Female Proteolysis Humans Ubiquitin Gene Regulatory Networks Neural Networks, Computer
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