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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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The human DEPhOsphorylation database DEPOD: a 2015 update.

Guangyou Duan1, Xun Li1, Maja Köhn2

  • 1European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Nucleic Acids Research
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Summary
This summary is machine-generated.

The updated DEPOD database aids research by cataloging human phosphatases and their substrates. This resource facilitates understanding of phosphatase-kinase-substrate networks critical in health and disease.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Bioinformatics

Background:

  • Phosphatases are vital enzymes with largely unknown biological roles.
  • Identifying enzyme substrates remains a significant challenge in biological research.

Purpose of the Study:

  • To present an updated version of the human DEPhOsphorylation Database (DEPOD).
  • To support research into phosphatase-kinase-substrate networks by providing curated data.

Main Methods:

  • Manual curation of human phosphatases, protein/non-protein substrates, and dephosphorylation sites.
  • Integration of pathway involvement and external links to kinases and small molecule modulators.
  • Enhancement of the user interface, including an interactive phosphatase-substrate network with a 'highlight node' function.

Main Results:

  • DEPOD now includes expanded data on human phosphatases and substrates.
  • New signaling pathways and interacting proteins have been incorporated.
  • The database offers comprehensive searchability, including a BLAST application.

Conclusions:

  • The updated DEPOD database is a valuable, manually curated resource for studying human phosphatases and their roles.
  • Enhanced features improve data accessibility and network visualization for researchers.
  • DEPOD supports the elucidation of complex phosphatase-mediated cellular processes.