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Related Experiment Videos

Automatic target selection for structural genomics on eukaryotes.

Jinfeng Liu1, Hedi Hegyi, Thomas B Acton

  • 1CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.

Proteins
|June 24, 2004
PubMed
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Structural genomics aims to determine protein structures for all families. The NorthEast Structural Genomics consortium (NESG) developed a method to identify and target eukaryotic protein domains for structure determination, suggesting over 40,000 structures are needed.

Area of Science:

  • Structural biology
  • Genomics
  • Bioinformatics

Background:

  • Structural genomics initiatives aim to experimentally determine protein structures for all families.
  • High-throughput structure determination is being investigated by multiple pilot projects.
  • The NorthEast Structural Genomics consortium (NESG) focuses on eukaryotic protein domain families.

Purpose of the Study:

  • To develop an automatic target selection procedure for identifying eukaryotic protein domain families.
  • To discard families with existing structural information in the Protein Data Bank (PDB).
  • To select representative families for structure determination.

Main Methods:

  • Proteins were dissected into structural domain-like regions.
  • A hierarchical approach (CHOP) utilized homology to PrISM, Pfam-A, and SWISS-PROT.

Related Experiment Videos

  • 103,796 eukaryotic proteins/ORFs were processed into 247,222 fragments.

    • Main Results:

    • 122,999 fragments were identified as suitable targets.
    • These fragments were grouped into over 27,000 singletons and over 18,000 multifragment clusters.
    • The study suggests over 40,000 structures are needed to cover five eukaryotic proteomes.

    Conclusions:

    • The developed method effectively identifies and categorizes protein domain fragments.
    • A significant number of protein structures need to be determined to cover eukaryotic proteomes.
    • This work contributes to the broader goals of structural genomics.