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Updated: Jul 5, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Protein structure databases with new web services for structural biology and biomedical research
Daron M Standley1, Akira R Kinjo, Kengo Kinoshita
1Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
Briefings in Bioinformatics
|April 24, 2008
Summary
Protein Data Bank Japan (PDBj) enhances protein structural data with functional and experimental details. Developed tools aid in recognizing protein homologies and assigning functions for structural genomics.
Area of Science:
- Structural biology
- Biochemistry
- Bioinformatics
Background:
- Protein Data Bank Japan (PDBj) is a key member of the worldwide Protein Data Bank (wwPDB).
- PDBj processes a significant portion (25-30%) of global protein structural data.
- Structural data is enriched with biological, biochemical, and experimental information.
Purpose of the Study:
- To present the applications developed at PDBj for structural biology and biomedical research.
- To showcase the utility of these tools in analyzing protein structures and functions.
Main Methods:
- Development of a Java-based molecular graphics viewer (jV).
- Implementation of electron density map visualization for quality assessment.
- Creation of eF-site (database of molecular surfaces) and eF-seek (similarity search service).
- Development of Protein Globe for accessing protein folds and linked applications.
- Identification of sequence and structural neighbors.
Main Results:
- Demonstration of tools for recognizing remote homologies between protein structures.
- Application of tools for assigning putative biochemical functions to new protein targets from structural genomics.
- Enhanced data curation and distribution by PDBj.
Conclusions:
- PDBj's developed applications are valuable resources for structural biology and biomedical studies.
- These tools facilitate the understanding of protein structure-function relationships.
- PDBj significantly contributes to the advancement of structural genomics research.
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