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Coverage of protein sequence space by current structural genomics targets.

Nicholas O'Toole1, Stéphane Raymond, Miroslaw Cygler

  • 1Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada.

Journal of Structural and Functional Genomics
|December 3, 2003
PubMed
Summary

Structural genomics aims to determine all protein structures. Current targets cover 44% of protein sequences, with significant overlap, aiding proteome structure determination.

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Area of Science:

  • Structural biology
  • Genomics
  • Bioinformatics

Background:

  • Structural genomics (SG) aims to determine the 3D structures of all proteins encoded by genomes.
  • Homology modeling, using known structures, is a primary method for predicting unknown protein structures.
  • Open exchange of SG target information facilitates analysis of sequence space coverage.

Purpose of the Study:

  • To analyze the coverage of protein sequence space by current structural genomics targets.
  • To evaluate the extent of existing or targeted structural data for entire proteomes.
  • To assess the overlap within the structural genomics target list.

Main Methods:

  • Analysis of sequences in the current structural genomics target list.
  • Determination of homologous sequences in the Protein Data Bank (PDB) and among SG targets.

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  • Mapping SG targets onto ProtoMap clusters of protein sequences.

    • Main Results:

    • Structural genomics targets cover approximately 44% of protein sequences classified by ProtoMap (over 150,000 sequences).
    • Coverage is high for small bacterial proteomes (e.g., H. influenzae) but lower for complex organisms (e.g., C. elegans).
    • SG targets show significant overlap, with one target typically in a cluster containing over six homologous targets.

    Conclusions:

    • Current structural genomics efforts provide substantial coverage of protein sequence space.
    • The overlap within target lists suggests redundancy and potential for optimization.
    • This analysis aids in evaluating the progress and strategic direction of structural genomics projects.