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Related Concept Videos

Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

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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...
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Protein Networks02:26

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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.
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Protein-protein Interfaces02:04

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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...
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Phosphorylation01:02

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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.
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Identification of Kinase-substrate Pairs Using High Throughput Screening
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Bioinformatics toolbox for exploring protein phosphorylation network.

Xing-Xing Shi1, Feng-Xu Wu2, Long-Can Mei2

  • 1College of Chemistry, Central China Normal University (CCNU).

Briefings in Bioinformatics
|July 16, 2020
PubMed
Summary
This summary is machine-generated.

This review surveys 19 bioinformatics tools for exploring phosphorylation networks, offering a comparative analysis to guide researchers in selecting the best tools for understanding cellular signaling and biological problems.

Keywords:
bioinformaticsphosphorylationphosphorylation networkvisualization

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Area of Science:

  • Biochemistry and Molecular Biology
  • Bioinformatics and Computational Biology

Background:

  • Understanding phosphorylation site interactions is crucial for cellular activity and signaling pathways.
  • Bioinformatics tools, particularly those with network visualization, aid in studying complex phosphorylation networks.

Purpose of the Study:

  • To provide a comprehensive toolbox for exploring phosphorylation networks.
  • To systematically survey and comparatively analyze available bioinformatics tools for phosphorylation network analysis.

Main Methods:

  • Conducted a systematic survey of 19 available bioinformatics tools for phosphorylation network exploration.
  • Performed a comparative analysis of these tools based on functionality, data sources, performance, visualization, and implementation.
  • Discussed application cases for the analyzed tools.

Main Results:

  • Identified and categorized 19 distinct bioinformatics tools for phosphorylation network analysis.
  • Provided a comparative summary of tool features, aiding in tool selection.
  • Highlighted the utility of these tools in various research scenarios.

Conclusions:

  • Easily accessible bioinformatics tools significantly facilitate biological discoveries in phosphorylation modification.
  • This review serves as a guide for researchers, students, and tool developers in the field of phosphorylation networks.