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Data growth and its impact on the SCOP database: new developments.

Antonina Andreeva1, Dave Howorth, John-Marc Chandonia

  • 1MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK.

Nucleic Acids Research
|November 15, 2007
PubMed
Summary
This summary is machine-generated.

The Structural Classification of Proteins (SCOP) database now efficiently handles growing protein structure data. New features facilitate faster discovery of protein relationships and families.

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • The Structural Classification of Proteins (SCOP) database organizes proteins by evolutionary and structural relationships.
  • SCOP's hierarchy includes levels such as Species, Protein, Family, Superfamily, Fold, and Class.
  • Rapid growth in structural data necessitates updates to SCOP's production methods.

Purpose of the Study:

  • To adapt the SCOP database production to manage the increasing volume of protein structural data.
  • To enhance the discovery of new evolutionary and structural relationships among proteins.
  • To introduce new features for improved accessibility and classification.

Main Methods:

  • Implemented a new update protocol for batch classification of protein structures.
  • Utilized detected relationships at Family and Superfamily levels for classification.
  • Introduced pre-SCOP, a developmental version for early access to new information.

Main Results:

  • SCOP now supports efficient batch classification, moving from sequential handling of data.
  • Pre-SCOP provides earlier access to emerging protein relationships and classifications.
  • The developments aim to keep pace with data generated by Structural Genomics initiatives.

Conclusions:

  • The revised SCOP production system effectively manages rapid growth in protein structural data.
  • New features in SCOP facilitate quicker identification of protein families and superfamilies.
  • Ongoing developments ensure SCOP remains a vital resource for structural biology research.