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Updated: Jun 19, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
PDBe: Protein Data Bank in Europe.
1Protein Databank in Europe, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. sameer@ebi.ac.uk
Nucleic Acids Research
|October 28, 2009
Summary
The Protein Data Bank in Europe (PDBe) enhances the global Protein Data Bank (PDB) archive with improved data quality and new services. Users can now explore protein structures and interactions through advanced querying and user-friendly interfaces.
Area of Science:
- Structural Biology
- Bioinformatics
- Data Archiving
Background:
- The Protein Data Bank (PDB) is a crucial archive for bio-macromolecular structure data.
- Enhancing data quality and consistency is vital for structural biology research.
- The Protein Data Bank in Europe (PDBe) collaborates globally to maintain and improve the PDB.
Purpose of the Study:
- To enhance the quality and consistency of the international PDB archive.
- To develop new services for accessing and querying structural data.
- To integrate curated derived data with existing structural information.
Main Methods:
- Developed a new database infrastructure using remediated PDB archive data.
- Created a specialized database for protein-ligand interactions.
- Implemented new services for textual and 3D structure-based queries.
- Designed user-friendly 'PDBeView Atlas pages' for PDB entry overviews.
Main Results:
- Improved quality and consistency of the PDB archive.
- New database infrastructure supporting enhanced data management.
- Advanced querying capabilities for users.
- User-friendly interfaces for data exploration.
- Enhanced tools for structure deposition and analysis through community involvement.
Conclusions:
- PDBe has successfully upgraded its infrastructure and services for the PDB.
- New tools facilitate easier access and analysis of bio-macromolecular structures.
- Collaboration with scientific communities drives continuous improvement in structural data archiving.
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