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An object-oriented database for protein structure analysis.

P M Gray1, N W Paton, G J Kemp

  • 1Department of Computing Science, University of Aberdeen, King's College, UK.

Protein Engineering
|March 1, 1990
PubMed
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An object-oriented database stores protein structure data, queried via Prolog or Daplex. This system excels at complex protein structure analysis and modeling, outperforming relational databases.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Database Systems

Background:

  • Storing and querying complex protein structure data presents challenges for traditional databases.
  • Relational databases struggle with the intricate relationships inherent in protein structural information.

Purpose of the Study:

  • To develop and evaluate an object-oriented database system for protein structure data.
  • To enable efficient querying and analysis of protein structural information using logic and query languages.

Main Methods:

  • Implemented an object-oriented database system to store protein primary, secondary, and tertiary structures.
  • Utilized the logic programming language Prolog and the query language Daplex for data retrieval and analysis.
  • Integrated complex calculations and routines within the database for user sharing.

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Main Results:

  • The system successfully stores and queries diverse protein structure data.
  • Queries navigate object networks representing protein structures.
  • Prolog and Daplex routines facilitate complex calculations and data integration.
  • Demonstrated utility in identifying loops and anchor positions for homologous protein modeling.

Conclusions:

  • Object-oriented databases are superior to relational databases for protein structure data management and complex query answering.
  • The developed system is well-suited for prototyping and advanced structural bioinformatics applications.