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SCOP database in 2002: refinements accommodate structural genomics.

Loredana Lo Conte1, Steven E Brenner, Tim J P Hubbard

  • 1MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK. loredana@mrc-lmb.cam.ac.uk

Nucleic Acids Research
|December 26, 2001
PubMed
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The Structural Classification of Proteins (SCOP) database now offers standardized access and management for protein structures. New features include unique identifiers and parseable files for improved protein domain classification and accessibility.

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 species, families, superfamilies, folds, and classes.
  • Increasing structural genomics projects necessitate robust database management and access.

Purpose of the Study:

  • To standardize access to the SCOP database.
  • To provide a foundation for managing a growing number of protein structures.
  • To enhance the usability and accessibility of protein domain classification data.

Main Methods:

  • Introduction of a new set of unique identifiers for each entry.
  • Development of a compact representation for protein domain classification.

Related Experiment Videos

  • Creation of new parseable files detailing SCOP domains and hierarchy.
  • Updates to the SCOP search engine and addition of external resource links.

    • Main Results:

    • Standardized access to the SCOP database.
    • Improved management of protein structural data.
    • Enhanced protein domain classification through new identifiers and files.
    • The ASTRAL compendium now reflects these new features.

    Conclusions:

    • The updated SCOP database provides enhanced, standardized access to protein structural information.
    • New features facilitate the management of large-scale structural genomics data.
    • Improved data organization and accessibility benefit the broader scientific community.