is an Aggregator.
PDBe-KB (Protein Data Bank in Europe - Knowledge Base) is an open, collaborative consortium for integration and enrichment of 3D-structure data and functional annotations to enable basic and translational research. It provides comprehensive access to macromolecular structure data integrated with functional annotations from multiple sources.
biomedical, genomics, proteomics, anatomy and development
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| pdbe.kb-portal | PDBe-KB Web Portal | pdbe-kb | GraphicalInterface | http | PDBe-KB web portal providing access t... |
| pdbe.kb-graph-database.neo4j3 | PDBe-KB Graph Database for Neo4J 3.5 | graphdb | GraphProduct | neo4j | Neo4j graph database containing integ... |
| pdbe.kb-graph-database.neo4j4 | PDBe-KB Graph Database for Neo4J 4 | graphdb | GraphProduct | neo4j | Neo4j graph database containing integ... |
| pdbe.kb-api | PDBe-KB Graph API | pdbe_doc | ProgrammingInterface | http | RESTful API powered by the PDBe-KB gr... |
| pdbe.kb-ftp | PDBe-KB FTP Archive | pdbe-kb | Product | http | FTP archive providing bulk download a... |
| pdbe.download-service | PDBe Download Service | docs | Product | mixed | Downloadable coordinate files, experi... |
| pdbe.sifts | SIFTS Residue-level Mapping | docs | Product | xml | SIFTS (Structure Integration with Fun... |
| pdbe.kb-manual | PDBe-KB User Manual | pdbe-kb-manual | DocumentationProduct | http | User guides and documentation for PDB... |
| pdbe.kb-schema | PDBe Graph Database Schema Explorer | schema | DocumentationProduct | http | Interactive schema explorer for the P... |
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| rnacentral.portal | RNAcentral Portal | rnacentral.org | GraphicalInterface | http | Web portal for searching and browsing... |
| rnacentral.api | RNAcentral REST API | api | ProgrammingInterface | http | REST API for programmatic access to R... |
| rnacentral.ftp | RNAcentral FTP Archive | RNAcentral | Product | http | FTP archive with current and archived... |
| rnacentral.public-db | RNAcentral Public Postgres Database | public-database | DataModelProduct | postgres | Public PostgreSQL database for direct... |
| genecards.protein.structures ⚠ | GeneCards Protein Structure Data | www.genecards.org | Product | http | Protein structure data from PDB Europ... |
| goa.pdb ⚠ | PDB GOA Annotations | PDB | Product | txt | GO annotations for PDB entries |
PDBe-KB (Protein Data Bank in Europe - Knowledge Base) is an open, collaborative consortium for integration and enrichment of 3D-structure data and functional annotations to enable basic and translational research.
The PDBe-KB graph database is implemented in Neo4J and represents each PDB entry as a tree structure:
This graph structure enables straightforward transfer of annotations between PDB entries mapping to the same UniProt accession and highly identical UniProt accessions.
If you use this resource, please cite:
PDBe-KB consortium. PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Research, Database Issue (2022). https://doi.org/10.1093/nar/gkab988
All data is freely available for both academic and commercial use under Creative Commons Attribution 4.0 (CC BY 4.0) license.
Created: September 09, 2025 | Last modified: October 08, 2025