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Related Experiment Videos

ISSD Version 2.0: taxonomic range extended

I A Adzhubei1, A A Adzhubei

  • 1Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119899 Moscow, Russia.

Nucleic Acids Research
|December 10, 1998
PubMed
Summary
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The Integrated Sequence-Structure Database (ISSD) now includes bacterial and yeast proteins, confirming sequence-structure correlations. This updated database aids research into mRNA codon usage and protein structure relationships.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • The Integrated Sequence-Structure Database (ISSD) integrates sequence and structure information.
  • Understanding correlations between mRNA synonymous codon usage and protein 3D structure is crucial for biological research.
  • Previous versions of ISSD focused primarily on mammalian proteins.

Purpose of the Study:

  • To expand the Integrated Sequence-Structure Database (ISSD) to include proteins from diverse taxonomic groups, specifically bacteria and yeast.
  • To validate the representative nature of ISSD data against organism-specific codon usage databases.
  • To confirm the presence of previously observed sequence-structure correlations in the expanded dataset.

Main Methods:

  • Addition of 88 Escherichia coli and 25 Saccharomyces cerevisiae proteins to the ISSD.

Related Experiment Videos

  • Comparison of ISSD sequences with codon usage data from the CUTG database.
  • Statistical analysis of sequence-structure correlations within the upgraded ISSD (Version 2.0).

    • Main Results:

    • ISSD Version 2.0 now contains mammalian, bacterial (E. coli), and yeast (S. cerevisiae) proteins.
    • ISSD sequences represent a valid subset of GenBank coding sequences.
    • Preliminary analyses confirm sequence-structure correlations in the expanded dataset, including bacterial and yeast proteins.

    Conclusions:

    • The expanded ISSD (Version 2.0) provides a more comprehensive resource for studying sequence-structure relationships across different organisms.
    • The database confirms the universality of sequence-structure correlations, extending beyond mammalian systems.
    • An improved web-based search and retrieval system enhances accessibility to ISSD data.