Info
3D-Beacons is a federated network providing unified access to both experimental and computationally predicted protein structure models. Hub hosted at EMBL-EBI, led by PDBe. Aggregates data from: PDBe, AlphaFold DB, SWISS-MODEL, Protein Ensemble Database (PED), SASBDB, Genome3D, and PDBe-KB. Users query via UniProt accession numbers.
People
| Name | Role | Affiliation |
|---|---|---|
| Sameer Velankar | Lead (PDBe Team Leader) | PDBe / EMBL-EBI |
| Mihaly Varadi | Project/data management, webpage design | PDBe / AlphaFold DB |
| Sreenath Nair | Lead developer (Hub API, registry) | PDBe / EMBL-EBI |
| Ian Sillitoe | Developer (Genome3D beacon) | UCL |
| Torsten Schwede | SWISS-MODEL provider | University of Basel |
| Christine Orengo | Genome3D provider | UCL |
Funding
- Funded through PDBe and RCSB PDB core operations grants (NSF, BBSRC, Wellcome)
Key Relationships
- Hub at PDBe / EMBL-EBI
- Federated providers include SASBDB (Dmitri Svergun), SWISS-MODEL (Torsten Schwede)
- Integrated into PDBe-KB aggregated protein views
- Mol* used as the 3D viewer
- AlphaFold DB (also at EMBL-EBI) is a major provider
Why this matters
3D-Beacons is the first federated attempt to unify experimental and predicted structural models under one API. It represents the emerging governance model for how predicted structures (AlphaFold, SWISS-MODEL) interact with experimental data (PDB, EMDB, SASBDB).
Key Reference
Varadi et al., GigaScience 11, giac118 (2022)