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The evolution of structural databases.

Oliviero Carugo1, Sándor Pongor

  • 1Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, Padriciano 99, 34012 Trieste, Italy. carugo@icgeb.trieste.it

Trends in Biotechnology
|November 22, 2002
PubMed
Summary

The Protein Data Bank (PDB) spurred the development of numerous structural databases. Improved interfaces and integrated information are crucial for helping users navigate these valuable resources effectively.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Data Science

Background:

  • The Protein Data Bank (PDB) serves as a foundational resource for structural data.
  • The proliferation of secondary structural databases has increased accessibility for specialists.
  • Non-specialist users face challenges due to the abundance and overlap of these databases.

Purpose of the Study:

  • To address the 'embarrassment of riches' in structural databases for non-specialist users.
  • To explore strategies for improving user navigation and data accessibility across multiple structural repositories.
  • To enhance the utility and customer base of structural data resources.

Main Methods:

  • Analysis of the evolution of structural databases from the PDB.
  • Evaluation of the current landscape of secondary structural databases.

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  • Conceptualization of improved interface designs and information integration strategies.

    • Main Results:

    • A significant increase in specialized structural databases has occurred.
    • Current database structures pose accessibility challenges for non-expert users.
    • Efficient interfaces and centralized information are identified as key solutions.

    Conclusions:

    • Integrating information within central repositories can guide users effectively.
    • Enhanced accessibility is vital for the sustained growth and utility of structural databases.
    • Streamlined access to structural data benefits both structural biologists and bioinformaticians.