AIMC Topic: Phosphorylation

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Modulatory role of garlicin in migration and invasion of intrahepatic cholangiocarcinoma via PI3K/AKT pathway.

International journal of clinical and experimental pathology
Increasing evidences have indicated the role of garlicin in inhibiting the progression of various tumors including glioma, pulmonary carcinoma and pancreatic carcinoma, via mediating cell apoptosis or cell cycle. The regulatory effect and related mol...

Systematic Analysis and Prediction of In Situ Cross Talk of O-GlcNAcylation and Phosphorylation.

BioMed research international
Reversible posttranslational modification (PTM) plays a very important role in biological process by changing properties of proteins. As many proteins are multiply modified by PTMs, cross talk of PTMs is becoming an intriguing topic and draws much at...

jEcho: an Evolved weight vector to CHaracterize the protein's posttranslational modification mOtifs.

Interdisciplinary sciences, computational life sciences
Protein's posttranslational modification (PTM) represents a major dynamic regulation of protein functions after the translation of polypeptide chains from mRNA molecule. Compared with the costly and labor-intensive wet laboratory characterization of ...

MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.

Nature methods
Protein phosphorylation is important in cellular pathways and altered in disease. We developed MIMP (http://mimp.baderlab.org/), a machine learning method to predict the impact of missense single-nucleotide variants (SNVs) on kinase-substrate interac...

Using support vector machines to identify protein phosphorylation sites in viruses.

Journal of molecular graphics & modelling
Phosphorylation of viral proteins plays important roles in enhancing replication and inhibition of normal host-cell functions. Given its importance in biology, a unique opportunity has arisen to identify viral protein phosphorylation sites. However, ...

Inter-species pathway perturbation prediction via data-driven detection of functional homology.

Bioinformatics (Oxford, England)
MOTIVATION: Experiments in animal models are often conducted to infer how humans will respond to stimuli by assuming that the same biological pathways will be affected in both organisms. The limitations of this assumption were tested in the IMPROVER ...

DeepPhosPPI: a deep learning framework with attention-CNN and transformer for predicting phosphorylation effects on protein-protein interactions.

Briefings in bioinformatics
Protein phosphorylation regulates protein function and cellular signaling pathways, and is strongly associated with diseases, including neurodegenerative disorders and cancer. Phosphorylation plays a critical role in regulating protein activity and c...

Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.

Bioinformatics (Oxford, England)
MOTIVATION: The rapid and extensive transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an unprecedented global health emergency, affecting millions of people and causing an immense socioeconomic impact. The id...

EMBER: multi-label prediction of kinase-substrate phosphorylation events through deep learning.

Bioinformatics (Oxford, England)
MOTIVATION: Kinase-catalyzed phosphorylation of proteins forms the backbone of signal transduction within the cell, enabling the coordination of numerous processes such as the cell cycle, apoptosis, and differentiation. Although on the order of 105 p...

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
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...