PDBe Knowledge Base
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.
[]
[{"category": "GraphicalInterface", "description": "PDBe-KB web portal providing access to enriched 3D structure data with functional annotations, including protein structures, ligand superpositions, and biological context", "format": "http", "id": "pdbe.kb-portal", "name": "PDBe-KB Web Portal", "product_url": "https://www.ebi.ac.uk/pdbe/pdbe-kb/"}, {"category": "GraphProduct", "description": "Neo4j graph database containing integrated PDBe-KB data with PDB entries, chains, entities, residues, and functional annotations. This version (graph.db.tgz) is for Neo4J 3.5.", "format": "neo4j", "id": "pdbe.kb-graph-database.neo4j3", "name": "PDBe-KB Graph Database for Neo4J 3.5", "product_url": "https://ftp.ebi.ac.uk/pub/databases/msd/graphdb/"}, {"category": "GraphProduct", "description": "Neo4j graph database containing integrated PDBe-KB data with PDB entries, chains, entities, residues, and functional annotations. This version (neo4j.dump) is for Neo4J 4 and above.", "format": "neo4j", "id": "pdbe.kb-graph-database.neo4j4", "name": "PDBe-KB Graph Database for Neo4J 4", "product_url": "https://ftp.ebi.ac.uk/pub/databases/msd/graphdb/"}, {"category": "ProgrammingInterface", "description": "RESTful API powered by the PDBe-KB graph database, providing programmatic access to structural data and functional annotations", "format": "http", "id": "pdbe.kb-api", "name": "PDBe-KB Graph API", "product_url": "https://www.ebi.ac.uk/pdbe/graph-api/pdbe_doc/"}, {"category": "Product", "description": "FTP archive providing bulk download access to PDBe-KB data files and annotations", "format": "http", "id": "pdbe.kb-ftp", "name": "PDBe-KB FTP Archive", "product_url": "http://ftp.ebi.ac.uk/pub/databases/pdbe-kb/"}, {"category": "Product", "description": "Downloadable coordinate files, experimental data files, validation reports, FASTA sequences, and small molecule data for PDB entries", "format": "mixed", "id": "pdbe.download-service", "name": "PDBe Download Service", "product_url": "https://www.ebi.ac.uk/pdbe/download/docs"}, {"category": "Product", "description": "SIFTS (Structure Integration with Function, Taxonomy and Sequences) provides residue-level mapping between UniProt and PDB entries", "format": "xml", "id": "pdbe.sifts", "name": "SIFTS Residue-level Mapping", "product_url": "https://www.ebi.ac.uk/pdbe/download/docs"}, {"category": "DocumentationProduct", "description": "User guides and documentation for PDBe-KB features and data access", "format": "http", "id": "pdbe.kb-manual", "name": "PDBe-KB User Manual", "product_url": "https://github.com/PDBe-KB/pdbe-kb-manual"}, {"category": "DocumentationProduct", "description": "Interactive schema explorer for the PDBe-KB Neo4j graph database, showing nodes, relationships, and data structure", "format": "http", "id": "pdbe.kb-schema", "name": "PDBe Graph Database Schema Explorer", "product_url": "https://www.ebi.ac.uk/pdbe/pdbe-kb/schema"}, {"category": "GraphicalInterface", "description": "Web portal for searching and browsing ncRNA sequences, structures, and annotations", "format": "http", "id": "rnacentral.portal", "name": "RNAcentral Portal", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/"}, {"category": "ProgrammingInterface", "description": "REST API for programmatic access to RNAcentral data", "format": "http", "id": "rnacentral.api", "name": "RNAcentral REST API", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/api"}, {"category": "Product", "description": "FTP archive with current and archived release files (sequences and annotations)", "format": "http", "id": "rnacentral.ftp", "name": "RNAcentral FTP Archive", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://ftp.ebi.ac.uk/pub/databases/RNAcentral"}, {"category": "DataModelProduct", "description": "Public PostgreSQL database for direct SQL access to RNAcentral data", "format": "postgres", "id": "rnacentral.public-db", "name": "RNAcentral Public Postgres Database", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/help/public-database"}, {"category": "Product", "description": "Protein structure data from PDB Europe and other structural databases", "format": "http", "id": "genecards.protein.structures", "name": "GeneCards Protein Structure Data", "original_source": ["pdbe"], "product_url": "https://www.genecards.org/", "warnings": ["File was not able to be retrieved when checked on 2026-01-30_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2026-01-28_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2026-02-04: HTTP 403 error when accessing file"]}, {"category": "Product", "description": "GO annotations for PDB entries", "format": "txt", "id": "goa.pdb", "name": "PDB GOA Annotations", "original_source": ["pdbe", "go"], "product_url": "ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/", "warnings": ["File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/'", "File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/'"]}]
{"activity_status": "active", "category": "Aggregator", "creation_date": "2025-09-09T00:00:00Z", "description": "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.", "domains": ["biomedical", "genomics", "proteomics", "anatomy and development"], "homepage_url": "https://www.ebi.ac.uk/pdbe/pdbe-kb/", "id": "pdbe", "last_modified_date": "2025-10-08T00:00:00Z", "layout": "resource_detail", "license": {"id": "https://creativecommons.org/licenses/by/4.0/", "label": "CC BY 4.0", "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png"}, "name": "PDBe Knowledge Base", "products": [{"category": "GraphicalInterface", "description": "PDBe-KB web portal providing access to enriched 3D structure data with functional annotations, including protein structures, ligand superpositions, and biological context", "format": "http", "id": "pdbe.kb-portal", "name": "PDBe-KB Web Portal", "product_url": "https://www.ebi.ac.uk/pdbe/pdbe-kb/"}, {"category": "GraphProduct", "description": "Neo4j graph database containing integrated PDBe-KB data with PDB entries, chains, entities, residues, and functional annotations. This version (graph.db.tgz) is for Neo4J 3.5.", "format": "neo4j", "id": "pdbe.kb-graph-database.neo4j3", "name": "PDBe-KB Graph Database for Neo4J 3.5", "product_url": "https://ftp.ebi.ac.uk/pub/databases/msd/graphdb/"}, {"category": "GraphProduct", "description": "Neo4j graph database containing integrated PDBe-KB data with PDB entries, chains, entities, residues, and functional annotations. This version (neo4j.dump) is for Neo4J 4 and above.", "format": "neo4j", "id": "pdbe.kb-graph-database.neo4j4", "name": "PDBe-KB Graph Database for Neo4J 4", "product_url": "https://ftp.ebi.ac.uk/pub/databases/msd/graphdb/"}, {"category": "ProgrammingInterface", "description": "RESTful API powered by the PDBe-KB graph database, providing programmatic access to structural data and functional annotations", "format": "http", "id": "pdbe.kb-api", "name": "PDBe-KB Graph API", "product_url": "https://www.ebi.ac.uk/pdbe/graph-api/pdbe_doc/"}, {"category": "Product", "description": "FTP archive providing bulk download access to PDBe-KB data files and annotations", "format": "http", "id": "pdbe.kb-ftp", "name": "PDBe-KB FTP Archive", "product_url": "http://ftp.ebi.ac.uk/pub/databases/pdbe-kb/"}, {"category": "Product", "description": "Downloadable coordinate files, experimental data files, validation reports, FASTA sequences, and small molecule data for PDB entries", "format": "mixed", "id": "pdbe.download-service", "name": "PDBe Download Service", "product_url": "https://www.ebi.ac.uk/pdbe/download/docs"}, {"category": "Product", "description": "SIFTS (Structure Integration with Function, Taxonomy and Sequences) provides residue-level mapping between UniProt and PDB entries", "format": "xml", "id": "pdbe.sifts", "name": "SIFTS Residue-level Mapping", "product_url": "https://www.ebi.ac.uk/pdbe/download/docs"}, {"category": "DocumentationProduct", "description": "User guides and documentation for PDBe-KB features and data access", "format": "http", "id": "pdbe.kb-manual", "name": "PDBe-KB User Manual", "product_url": "https://github.com/PDBe-KB/pdbe-kb-manual"}, {"category": "DocumentationProduct", "description": "Interactive schema explorer for the PDBe-KB Neo4j graph database, showing nodes, relationships, and data structure", "format": "http", "id": "pdbe.kb-schema", "name": "PDBe Graph Database Schema Explorer", "product_url": "https://www.ebi.ac.uk/pdbe/pdbe-kb/schema"}, {"category": "GraphicalInterface", "description": "Web portal for searching and browsing ncRNA sequences, structures, and annotations", "format": "http", "id": "rnacentral.portal", "name": "RNAcentral Portal", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/"}, {"category": "ProgrammingInterface", "description": "REST API for programmatic access to RNAcentral data", "format": "http", "id": "rnacentral.api", "name": "RNAcentral REST API", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/api"}, {"category": "Product", "description": "FTP archive with current and archived release files (sequences and annotations)", "format": "http", "id": "rnacentral.ftp", "name": "RNAcentral FTP Archive", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://ftp.ebi.ac.uk/pub/databases/RNAcentral"}, {"category": "DataModelProduct", "description": "Public PostgreSQL database for direct SQL access to RNAcentral data", "format": "postgres", "id": "rnacentral.public-db", "name": "RNAcentral Public Postgres Database", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/help/public-database"}, {"category": "Product", "description": "Protein structure data from PDB Europe and other structural databases", "format": "http", "id": "genecards.protein.structures", "name": "GeneCards Protein Structure Data", "original_source": ["pdbe"], "product_url": "https://www.genecards.org/", "warnings": ["File was not able to be retrieved when checked on 2026-01-30_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2026-01-28_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2026-02-04: HTTP 403 error when accessing file"]}, {"category": "Product", "description": "GO annotations for PDB entries", "format": "txt", "id": "goa.pdb", "name": "PDB GOA Annotations", "original_source": ["pdbe", "go"], "product_url": "ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/", "warnings": ["File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/'", "File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/'"]}], "publications": [{"id": "https://doi.org/10.1093/nar/gkab988", "preferred": true, "title": "PDBe-KB: collaboratively defining the biological context of structural data"}], "repository": "https://github.com/PDBe-KB"}