Completed Cells, Biochemistry & Physiology Chemistry

PDBe - Facilitating Open Science in Structural Biology

Funder Wellcome Charity-funded
Associated organisations European Bioinformatics Institute · European Molecular Biology Laboratory Europe PMC affiliations are not treated as award recipients or mapped locations.
Funding £1.4M
Period Feb 2020 — Jan 2025

In plain English

AI plain-English summary

The Protein Data Bank in Europe (PDBe) is upgrading the global archive of molecular structures to keep pace with a flood of new data from advanced imaging techniques. Structural biology—the science of mapping the 3D shapes of proteins, DNA, and other large molecules—has been transformed by methods such as cryo-electron microscopy, which can now capture structures at near-atomic resolution. These techniques generate far larger and more complex datasets than older methods. The PDBe, a founding member of the Worldwide Protein Data Bank (wwPDB), must update its deposition, validation, and curation systems (OneDep) to handle this influx, while maintaining data quality for all structures produced in Europe and Africa. If successful, the project will keep the PDB—the single global archive of macromolecular structures, established in 1971—functional and trustworthy. This matters because researchers worldwide rely on these structures to design drugs, understand diseases, and engineer enzymes. The work also includes developing better data-analysis tools, ensuring interoperability with specialist archives for experimental data, and conducting training and public engagement. While the impact is largely invisible to the public, it underpins much of modern biomedicine and biotechnology.

View original technical description
Established in 1971, the Protein Data Bank (PDB), is the single global archive of macromolecular structures. It is managed by the Worldwide Protein Data Bank (wwPDB), currently consisting of four partner sites across Europe, Asia and the USA. The Protein Data Bank in Europe (PDBe) is a founding member of wwPDB and is an ELIXIR Core Data Resource and deposition database. Structural biology is being transformed by rapid advances in structure-determination techniques (e.g. Electron Microscopy and Integrative/Hybrid Methods) and improved access to large-scale facilities that offer high-throughput methods (e.g. ligand and fragment screens). These developments lead to a continuous increase in the number, size and complexity of structures deposited to the PDB. In this project we aim to address the challenges posed by these advances in structural biology through: - Active engagement in worldwide data-archiving activities: - Development of data-representation standards; - Further development of the wwPDB deposition, validation, and biocuration system (OneDep) to accommodate new structure-determination modalities; - Interoperability with specialist archives for experimental structural biology data. - Maintaining data quality and integrity by fulfilling PDBe’s responsibility to curate all structures produced in Europe and Africa. - Development of data-analysis and dissemination tools for improved accessibility. - Conducting training, outreach, and public-engagement activities.

View the original record at the funder ↗

Researchers

Gerard Kleywegt (EPMC Awardee)Sameer Velankar (EPMC Awardee)

Related Research

Grants with similar aims, by meaning.

Protein Data Bank in Europe - an integrated resource for 3D molecular and cellular structure.
Protein Data Bank in Europe.
FunPDBe - enhancing structural and functional annotation of macromolecular structure data in the PDB by collaboration and integration
CIBR 19-BBSRC-NSF/BIO: Next generation PDB - FACT infrastructure with value added FAIR data supporting diverse research and education user communities
24BBR: Enabling efficient basic and translational research through sustainable expansion of PDBe Knowledge Base Using Integrative Resource Framework

Original classification

Biomedical Resources Grant

Plain English summaries and category classifications on this site are generated by AI and may not perfectly reflect the original research.