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Updated: Mar 31, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
16.2K
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.
Sameer Velankar1, Glen van Ginkel2, Younes Alhroub2
1Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK sameer@ebi.ac.uk.
Nucleic Acids Research
|October 18, 2015
Summary
The Protein Data Bank in Europe (PDBe) website redesign offers improved access to macromolecular structures. New features enhance data discovery and analysis for both expert and non-expert users.
Area of Science:
- Structural Biology
- Bioinformatics
- Data Science
Background:
- The Protein Data Bank in Europe (PDBe) is a crucial resource for macromolecular structure data.
- Effective dissemination and access to this data are vital for scientific advancement.
Purpose of the Study:
- To redesign the PDBe website for enhanced user experience and data accessibility.
- To integrate value-added information and improve data querying capabilities.
- To develop a RESTful API for unified access to structural data.
Main Methods:
- Website redesign based on user requirements analysis.
- Development of a new query system incorporating data-quality metrics.
- Implementation of a RESTful API for data access.
- Integration of citation data and open-access publication figures.
Main Results:
- Intuitive website access to enriched macromolecular structure information.
- Identification of 'best structures' using data-quality information.
- Unified access to PDB and EMDB data via a new API.
- Inclusion of literature references and publication figures linked to PDB entries.
Conclusions:
- The redesigned PDBe website and new API facilitate intuitive access to structural data.
- Enhanced data integration and querying support both novice and expert users.
- Improved access to structural information and associated literature accelerates research.
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