{"doi":"10.1093/nar/gkt1180","title":"PDBe: Protein Data Bank in Europe","abstract":"The Protein Data Bank in Europe (pdbe.org) is a founding member of the Worldwide PDB consortium (wwPDB; wwpdb.org) and as such is actively engaged in the deposition, annotation, remediation and dissemination of macromolecular structure data through the single global archive for such data, the PDB. Similarly, PDBe is a member of the EMDataBank organisation (emdatabank.org), which manages the EMDB archive for electron microscopy data. PDBe also develops tools that help the biomedical science community to make effective use of the data in the PDB and EMDB for their research. Here we describe new or improved services, including updated SIFTS mappings to other bioinformatics resources, a new browser for the PDB archive based on Gene Ontology (GO) annotation, updates to the analysis of Nuclear Magnetic Resonance-derived structures, redesigned search and browse interfaces, and new or updated visualisation and validation tools for EMDB entries.","journal":"Nucleic Acids Research","year":2013,"id":6613,"datarank":6.995258424678889,"base_score":5.0106352940962555,"endowment":5.0106352940962555,"self_citation_contribution":0.7515952941144385,"citation_network_contribution":6.2436631305644505,"self_endowment_contribution":0.7515952941144385,"citer_contribution":6.2436631305644505,"corpus_percentile":97.4239962868415,"corpus_rank":334,"citation_count":149,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9607,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2013-11-27","fair_score":56.0417,"fair_percentile":63.57615894039735,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":60787,"name":"Younes Alhroub","orcid":null,"position":1,"is_corresponding":false},{"id":60788,"name":"Gary M. Battle","orcid":null,"position":2,"is_corresponding":false},{"id":60789,"name":"John M. Berrisford","orcid":"0000-0003-4442-5871","position":3,"is_corresponding":false},{"id":60790,"name":"Estelle Bochet","orcid":null,"position":4,"is_corresponding":false},{"id":60791,"name":"Matthew J. Conroy","orcid":null,"position":5,"is_corresponding":false},{"id":60792,"name":"Jose M. Dana","orcid":"0000-0002-8362-8869","position":6,"is_corresponding":false},{"id":60793,"name":"Manuel A. Fernandez Montecelo","orcid":null,"position":7,"is_corresponding":false},{"id":60794,"name":"Glen van Ginkel","orcid":"0000-0002-9857-6459","position":8,"is_corresponding":false},{"id":60795,"name":"Swanand P. Gore","orcid":null,"position":9,"is_corresponding":false},{"id":60797,"name":"Rowan Hatherley","orcid":null,"position":11,"is_corresponding":false},{"id":60798,"name":"Pieter M.S. Hendrickx","orcid":null,"position":12,"is_corresponding":false},{"id":60799,"name":"Miriam Hirshberg","orcid":null,"position":13,"is_corresponding":false},{"id":60800,"name":"Ingvar Lagerstedt","orcid":"0000-0002-3346-4528","position":14,"is_corresponding":false},{"id":60801,"name":"Saqib Mir","orcid":"0000-0002-3778-916X","position":15,"is_corresponding":false},{"id":60802,"name":"Abhik Mukhopadhyay","orcid":"0000-0002-9808-7620","position":16,"is_corresponding":false},{"id":60803,"name":"Thomas J. Oldfield","orcid":null,"position":17,"is_corresponding":false},{"id":60804,"name":"Ardan Patwardhan","orcid":"0000-0001-7663-9028","position":18,"is_corresponding":false},{"id":60805,"name":"Luana Rinaldi","orcid":null,"position":19,"is_corresponding":false},{"id":60806,"name":"Gaurav Sahni","orcid":null,"position":20,"is_corresponding":false},{"id":60807,"name":"Eduardo Sanz-García","orcid":null,"position":21,"is_corresponding":false},{"id":60808,"name":"Sanchayita Sen","orcid":"0000-0002-3469-9249","position":22,"is_corresponding":false},{"id":60809,"name":"Robert A. Slowley","orcid":null,"position":23,"is_corresponding":false},{"id":33988,"name":"Sameer Velankar","orcid":"0000-0002-8439-5964","position":24,"is_corresponding":false},{"id":60810,"name":"Michael E. Wainwright","orcid":null,"position":25,"is_corresponding":false},{"id":33990,"name":"Gerard J. Kleywegt","orcid":"0000-0002-4670-0331","position":26,"is_corresponding":false},{"id":60811,"name":"M.J. Conroy","orcid":"0000-0001-7297-9623","position":27,"is_corresponding":false},{"id":60812,"name":"Swanand Gore","orcid":"0000-0001-7468-6269","position":28,"is_corresponding":false},{"id":60813,"name":"P. Haslam","orcid":"0000-0002-1683-9893","position":29,"is_corresponding":false},{"id":60814,"name":"P. Hendrickx","orcid":"0000-0002-1112-6624","position":30,"is_corresponding":false},{"id":60815,"name":"Eduardo Sanz‐García","orcid":"0000-0002-7166-191X","position":31,"is_corresponding":false},{"id":60786,"name":"Aleksandras Gutmanas","orcid":"0000-0001-6311-0176","position":0,"is_corresponding":true}],"reference_count":39,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"24288376","pmcid":"PMC3965016","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":80.0,"fair_i":37.5,"fair_r":41.6667,"fair_zscore":0.2955,"fair_rationale":{"fair_score":56.04,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":65.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper describes structured data (XML SIFTS, GO assignments) but provides no evidence of machine-readable metadata (e.g., schema.org, JSON-LD, RDF) for the paper itself."}]},"A":{"name":"Accessible","score":80.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":1.0,"signal":null,"rationale":"The paper describes multiple clear access protocols (pdbe.org, pdbe.org/sifts, addons.mozilla.org, ftp implied) and explicit downloadable XML for SIFTS."}]},"I":{"name":"Interoperable","score":37.5,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"The paper uses standard identifiers (PDB IDs, UniProt, GO, Pfam, CATH) and formats (XML, SOLR) but does not formally describe adherence to a machine-readable interoperability framework."}]},"R":{"name":"Reusable","score":41.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.667,"signal":null,"rationale":"The paper includes a CC BY license, states data availability via public archives (PDB, EMDB, SIFTS), and mentions SW download URLs, but lacks a formal data-availability statement for the paper's own derived data or reproducibility details for the tools."}]}},"suggestions":["Add structured metadata (e.g., JSON-LD or RDF) embedded in the paper HTML to describe the dataset and its licensing.","Include a formal data-availability statement and a persistent identifier (e.g., DOI) for the software tools described.","Provide a machine-readable description of the SIFTS XML schema or use a standard vocabulary (e.g., DCAT) to describe the data resources.","Add a clear license for the software tools (e.g., Apache 2.0) and a link to the source code repository.","Improve reproducibility by specifying exact version numbers of all databases and software referenced in the paper."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:38:09.974663Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}