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.
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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 | Relation | Description |
|---|---|---|---|---|---|---|
| rnacentral.portal | RNAcentral Portal | rnacentral.org | GraphicalInterface | http | had primary source | Web portal for searching and browsing... |
| rnacentral.api | RNAcentral REST API | api | ProgrammingInterface | http | had primary source | REST API for programmatic access to R... |
| rnacentral.ftp | RNAcentral FTP Archive | RNAcentral | Product | http | had primary source | FTP archive with current and archived... |
| rnacentral.public-db | RNAcentral Public Postgres Database | public-database | DataModelProduct | postgres | had primary source | Public PostgreSQL database for direct... |
| genecards.protein.structures ⚠ | GeneCards Protein Structure Data | www.genecards.org | Product | http | had primary source | Protein structure data from PDB Europ... |
| goa.pdb | PDB GOA Annotations | PDB | Product | txt | had primary source | GO annotations for PDB entries |
| intact.api | IntAct Web Service | ws | ProgrammingInterface | http | had primary source | IntAct web service and URL-based prog... |
| intact.ftp.psi25 | IntAct PSI-MI XML 2.5 | psi25 | Product | psi_mi_xml | had primary source | IntAct data in PSI-MI XML 2.5 format ... |
| intact.ftp.psi30 | IntAct PSI-MI XML 3.0 | psi30 | Product | psi_mi_xml | had primary source | IntAct data in PSI-MI XML 3.0 format ... |
| intact.ftp.psimitab | IntAct PSI-MI MITAB 2.7 | psimitab | Product | psi_mi_mitab | had primary source | IntAct data in PSI-MI MITAB format (d... |
| intact.ftp.psimitab.all | IntAct MITAB Archive | intact.zip (807.1 MB) | Product | psi_mi_mitab | had primary source | Entire MITAB export of the database a... |
| intact.datasets | IntAct Datasets | datasets | Product | http | had primary source | Curated and computational datasets (d... |
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