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Phosphorylation

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Linsitinib inhibits proliferation and induces apoptosis of both IGF-1R and TSH-R expressing cells.

Frontiers in immunology
BACKGROUND: The insulin-like growth factor 1 receptor (IGF-1R) and the thyrotropin receptor (TSH-R) are expressed on orbital cells and thyrocytes. These receptors are targeted in autoimmune-induced thyroid eye disease (TED). Effective therapeutic tre...

Res-GCN: Identification of protein phosphorylation sites using graph convolutional network and residual network.

Computational biology and chemistry
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...

DeepPhoPred: Accurate Deep Learning Model to Predict Microbial Phosphorylation.

Proteins
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...

Empirical Comparison and Analysis of Artificial Intelligence-Based Methods for Identifying Phosphorylation Sites of SARS-CoV-2 Infection.

International journal of molecular sciences
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...

GraphPhos: Predict Protein-Phosphorylation Sites Based on Graph Neural Networks.

International journal of molecular sciences
Phosphorylation is one of the most common protein post-translational modifications. The identification of phosphorylation sites serves as the cornerstone for protein-phosphorylation-related research. This paper proposes a protein-phosphorylation site...

Screening of Aβ and phosphorylated tau status in the cerebrospinal fluid through machine learning analysis of portable electroencephalography data.

Scientific reports
Diagnosing Alzheimer's disease (AD) through pathological markers is typically costly and invasive. This study aims to find a noninvasive, cost-effective method using portable electroencephalography (EEG) to detect changes in AD-related biomarkers in ...

MMFuncPhos: A Multi-Modal Learning Framework for Identifying Functional Phosphorylation Sites and Their Regulatory Types.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Protein phosphorylation plays a crucial role in regulating a wide range of biological processes, and its dysregulation is strongly linked to various diseases. While many phosphorylation sites have been identified so far, their functionality and regul...

Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites.

Nature communications
Mass spectrometry-based phosphoproteomics offers a comprehensive view of protein phosphorylation, yet our limited knowledge about the regulation and function of most phosphosites hampers the extraction of meaningful biological insights. To address th...

Machine learning-based prediction reveals kinase MAP4K4 regulates neutrophil differentiation through phosphorylating apoptosis-related proteins.

PLoS computational biology
Neutrophils, an essential innate immune cell type with a short lifespan, rely on continuous replenishment from bone marrow (BM) precursors. Although it is established that neutrophils are derived from the granulocyte-macrophage progenitor (GMP), the ...

Insights into phosphorylation-induced influences on conformations and inhibitor binding of CDK6 through GaMD trajectory-based deep learning.

Physical chemistry chemical physics : PCCP
The phosphorylation of residue T177 produces a significant effect on the conformational dynamics of CDK6. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) are applied to explore the molecular mechanism of the ...