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Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large

Akira R Kinjo1, Gert-Jan Bekker2, Hirofumi Suzuki2

  • 1Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan akinjo@protein.osaka-u.ac.jp.

Nucleic Acids Research
|October 30, 2016
PubMed
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Protein Data Bank Japan (PDBj) offers updated tools and services for analyzing macromolecular structures. Enhanced data interoperability and new features improve access to protein structure information.

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Biochemistry

Background:

  • Protein Data Bank Japan (PDBj) is a key member of the worldwide Protein Data Bank (wwPDB) network.
  • PDBj archives experimentally determined macromolecular structures and provides analytical tools.

Purpose of the Study:

  • To outline updated web interfaces, RESTful web services, and backend database supporting PDBj services.
  • To describe enhancements in data interoperability and services for analyzing large structures from hybrid methods.

Main Methods:

  • Development of updated web user interfaces and RESTful web services.
  • Implementation of a backend relational database.
  • Enhancement of wwPDB/RDF data connectivity with external resources.

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Main Results:

  • Updated PDBj infrastructure supporting enhanced data access and analysis.
  • Improved interoperability of macromolecular structural data through wwPDB/RDF.
  • New services for searching, comparing, and analyzing large structures, particularly those determined by hybrid methods.

Conclusions:

  • PDBj continues to evolve, offering advanced tools and services for the structural biology community.
  • Enhanced data integration and accessibility facilitate deeper understanding of protein structures and functions.