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Updated: Jul 23, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)
Akira R Kinjo1, Gert-Jan Bekker1, Hiroshi Wako2
1Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Protein Science : a Publication of the Protein Society
|August 18, 2017
Summary
Protein Data Bank Japan (PDBj) enhances macromolecular structure data services with new tools like PDBj Mine 2 and Molmil. These updates improve data archiving, analysis, and accessibility for researchers worldwide.
Area of Science:
- Structural biology
- Bioinformatics
- Biochemistry
Background:
- Protein Data Bank Japan (PDBj) is a key member of the worldwide Protein Data Bank (wwPDB).
- PDBj archives experimentally determined biological macromolecular structures.
- PDBj offers unique services and tools for data analysis and access.
Purpose of the Study:
- To report on new and updated services and tools provided by PDBj.
- To enhance the accessibility and analysis capabilities of macromolecular structure data.
- To integrate PDBj services with other biological databases.
Main Methods:
- Development and integration of new tools: RDB PDBj Mine 2, Molmil (WebGL molecular viewer), ProMode-Elastic server, virtual reality system for eF-site analysis.
- Extension of existing services: Omokage search for molecular shape similarity.
- Integration of PDBj and Biological Magnetic Resonance Data Bank (BMRB) searches.
Main Results:
- Introduction of PDBj Mine 2 for enhanced data mining.
- Deployment of Molmil for interactive 3D molecular visualization.
- Availability of ProMode-Elastic for normal mode analysis of protein dynamics.
- New virtual reality system for visualizing protein electrostatic surfaces.
- Improved Omokage search for molecular shape similarity.
- Integrated search functionality between PDBj and BMRB.
Conclusions:
- PDBj continues to innovate and expand its offerings for structural biology research.
- The new tools and integrated services enhance data usability and analytical power.
- These advancements facilitate deeper understanding of biological macromolecular structures and functions.
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