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Related Experiment Videos

SCOP database in 2004: refinements integrate structure and sequence family data.

Antonina Andreeva1, Dave Howorth, Steven E Brenner

  • 1MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK.

Nucleic Acids Research
|December 19, 2003
PubMed
Summary

The Structural Classification of Proteins (SCOP) database classifies proteins by evolutionary and structural relationships. Recent updates refine this classification and enhance database integration and dynamic linking capabilities.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Protein science

Background:

  • The Structural Classification of Proteins (SCOP) database organizes proteins based on evolutionary and structural relationships.
  • Protein domains are hierarchically classified into families, superfamilies, folds, and classes.
  • Accumulating sequence and structural data necessitates rigorous analysis for understanding protein evolution.

Purpose of the Study:

  • To refine the SCOP classification system, introducing changes primarily below the superfamily level.
  • To rationalize and integrate protein data across multiple sequence and structure databases.
  • To modernize SCOP's interface for enhanced dynamic linking with other biological databases.

Main Methods:

  • Hierarchical classification of protein domains into families, superfamilies, folds, and classes.

Related Experiment Videos

  • Refinement of the SCOP classification starting from release 1.63.
  • Development of dynamic linking capabilities within the SCOP interface.

    • Main Results:

    • Initiation of a gradual reclassification of SCOP entries, with changes mainly affecting levels below superfamily.
    • Integration of SCOP data with other protein sequence and structure databases.
    • Expansion of static links and introduction of dynamic linking for SCOP domain entries.

    Conclusions:

    • The ongoing refinement of SCOP classification improves the understanding of protein structures and evolution.
    • Enhanced data integration and dynamic linking facilitate more comprehensive analysis of protein information.
    • SCOP continues to evolve as a vital resource for the protein science community.