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CutDB: a proteolytic event database.

Yoshinobu Igarashi1, Alexey Eroshkin, Svetlana Gramatikova

  • 1Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.

Nucleic Acids Research
|December 5, 2006
PubMed
Summary
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CutDB is a new database that systematically collects and organizes information on proteolytic events, which are crucial for many biological processes. This resource aims to make data on proteases, protein substrates, and cleavage sites easily accessible for research.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Bioinformatics

Background:

  • Proteolytic events, mediated by proteases, are essential for numerous biological regulatory processes beyond simple protein degradation.
  • Information regarding specific proteolytic events is currently fragmented across numerous publications, hindering large-scale analysis.
  • A centralized, accessible resource for proteolytic event data is needed to facilitate research in molecular biology and disease pathology.

Purpose of the Study:

  • To create CutDB, a comprehensive and accessible database of documented proteolytic events.
  • To integrate data on proteases, their protein substrates, and specific cleavage sites.
  • To provide a platform for systematic analysis and community-driven expansion of proteolytic event knowledge.

Main Methods:

Related Experiment Videos

  • Systematic collection and curation of proteolytic events from public archives (MEROPS, HPRD) and scientific literature.
  • Definition of a CutDB entry by the unique combination of protease, protein substrate, and cleavage site.
  • Development of a user-friendly interface for data input, search, and visualization, including network diagrams.

Main Results:

  • CutDB currently integrates 3,070 proteolytic events involving 470 distinct proteases.
  • The database supports diverse search functionalities and data visualization tools.
  • A community annotation approach, inspired by Wikipedia, enables user contributions and accelerates content expansion.

Conclusions:

  • CutDB represents a significant advancement in organizing and accessing information on proteolytic events.
  • The database facilitates research into the roles of proteases in both normal physiological conditions and pathological states.
  • The community-driven model promises rapid growth and comprehensive coverage of proteolytic events in molecular biology.