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Updated: May 5, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
PDBe: Protein Data Bank in Europe
Aleksandras Gutmanas1, Younes Alhroub, Gary M Battle
1Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
The Protein Data Bank in Europe (PDBe) enhances access to macromolecular structure data. New tools and improved interfaces aid researchers using the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB).
Area of Science:
- Structural Biology
- Bioinformatics
- Data Archiving
Background:
- The Protein Data Bank in Europe (PDBe) is a key member of the Worldwide Protein Data Bank (wwPDB) and EMDataBank.
- PDBe facilitates the deposition, annotation, and dissemination of macromolecular structure data.
- PDBe develops tools to support the biomedical science community's use of structural data.
Purpose of the Study:
- To describe new and improved services offered by PDBe.
- To enhance user access and utility of the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) archives.
- To detail advancements in data integration, visualization, and validation tools.
Main Methods:
- Updating SIFTS mappings for cross-resource integration.
- Developing a Gene Ontology (GO) annotation-based browser for the PDB archive.
- Enhancing analysis of Nuclear Magnetic Resonance (NMR) structures.
- Redesigning search and browse interfaces.
- Updating visualization and validation tools for EMDB entries.
Main Results:
- Improved SIFTS mappings provide better integration with other bioinformatics resources.
- A new GO-based browser enhances PDB archive exploration.
- NMR structure analysis has been updated.
- Redesigned interfaces offer improved user experience for searching and browsing data.
- New and updated tools enhance visualization and validation of EMDB entries.
Conclusions:
- PDBe continues to innovate, providing essential services for accessing and utilizing macromolecular structure data.
- The enhancements aim to empower biomedical researchers with more effective tools for data exploration and analysis.
- These updates strengthen PDBe's role in supporting structural biology research globally.
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