Related Experiment Video
Updated: May 27, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
PDBe: Protein Data Bank in Europe
S Velankar1, Y Alhroub, C Best
1Protein Data Bank in Europe, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Nucleic Acids Research
|November 24, 2011
Summary
The Protein Data Bank in Europe (PDBe) enhances access to biomacromolecular structure data. New tools like PDBportfolio and UniPDB improve visualization and data exploration for researchers.
Area of Science:
- Structural Biology
- Bioinformatics
- Biotechnology
Background:
- The Protein Data Bank in Europe (PDBe) is a key partner in the Worldwide Protein Data Bank (wwPDB) organization.
- PDBe manages the global archive of biomacromolecular structure data.
- There is a continuous need to improve accessibility of structural data for the biomedical community.
Purpose of the Study:
- To describe recently developed, extended, or improved services by PDBe.
- To enhance the accessibility and utility of biomacromolecular structure data.
- To support researchers in the biomedical community through advanced data visualization and exploration tools.
Main Methods:
- Development of an animated structure-presentation widget (PDBportfolio).
- Creation of a widget to display UniProt sequence coverage in the Protein Data Bank (PDB) (UniPDB).
- Implementation of chemistry- and taxonomy-based PDB archive browsers (PDBeXplore).
- Development of an interactive visualization tool for NMR structures and associated data (Vivaldi).
Main Results:
- PDBe has successfully developed and deployed new tools to aid in the exploration of structural data.
- PDBportfolio offers animated presentations of molecular structures.
- UniPDB provides graphical visualization of sequence coverage.
- PDBeXplore enables browsing the PDB archive by chemical and taxonomic classifications.
- Vivaldi facilitates interactive visualization of NMR data and analysis results.
Conclusions:
- The newly developed and improved services by PDBe significantly enhance the accessibility of biomacromolecular structure data.
- These tools empower the biomedical community with advanced capabilities for data analysis, visualization, and exploration.
- PDBe continues to play a vital role in advancing structural biology research through innovative resource development.
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These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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The primary structure of a protein is its amino acid sequence.
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