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Related Concept Videos

Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Phosphorylation01:02

Phosphorylation

The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
During phosphorylation, protein kinases transfer the terminal phosphate group of ATP to specific amino acid side chains of substrate proteins. Serine, threonine, and tyrosine are the most commonly...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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Related Experiment Video

Updated: May 9, 2026

Identification of Kinase-substrate Pairs Using High Throughput Screening
11:13

Identification of Kinase-substrate Pairs Using High Throughput Screening

Published on: August 29, 2015

PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data.

Wei-Ming Chen1, Samuel A Danziger, Jung-Hsien Chiang

  • 1Institute for Systems Biology, Seattle, WA 98109-5234, USA, Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan and Seattle Biomedical Research Institute, Seattle, WA 98109-5219, USA.

Bioinformatics (Oxford, England)
|July 9, 2013
PubMed
Summary

PhosphoChain predicts protein phosphorylation and signaling networks by integrating mRNA expression and motif detection. This tool identifies more phosphorylation sites and kinase-phosphatase interactions than existing methods.

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A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors
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A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors

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Related Experiment Videos

Last Updated: May 9, 2026

Identification of Kinase-substrate Pairs Using High Throughput Screening
11:13

Identification of Kinase-substrate Pairs Using High Throughput Screening

Published on: August 29, 2015

A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors
10:17

A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors

Published on: April 29, 2022

Area of Science:

  • Molecular Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Protein phosphorylation regulates crucial cellular activities and information transmission via signaling networks.
  • Predicting phosphorylation and signaling networks is challenging and lags behind transcriptional network prediction.

Purpose of the Study:

  • To develop PhosphoChain, a novel computational framework for predicting kinases, phosphatases, and phosphorylation event chains in signaling networks.
  • To improve the accuracy of phosphorylation site and kinase-phosphatase interaction predictions.

Main Methods:

  • PhosphoChain integrates mRNA expression levels of regulators and targets with a motif detection algorithm.
  • Optional prior biological information can be incorporated into the prediction model.
  • The method was validated using yeast signaling pathway data and phosphoproteomic datasets.

Main Results:

  • PhosphoChain accurately reconstructed approximately 78% of the yeast mitogen-activated protein kinase pathway.
  • It identified approximately 27% more phosphorylation sites compared to existing tools like NetPhosYeast and GPS2.0.
  • Predictions of kinase-phosphatase interactions showed a 59% overlap with known yeast database interactions.

Conclusions:

  • PhosphoChain offers a robust framework for predicting condition-specific phosphorylation events from high-throughput data.
  • The tool enhances the understanding of cellular signaling pathways through improved prediction accuracy.