{"doi":"10.1093/nar/gku1214","title":"The RCSB Protein Data Bank: views of structural biology for basic and applied research and education","abstract":"The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine.","journal":"Nucleic Acids Research","year":2014,"id":1994,"datarank":10.236884066478307,"base_score":6.289715570908998,"endowment":6.289715570908998,"self_citation_contribution":0.9434573356363498,"citation_network_contribution":9.293426730841958,"self_endowment_contribution":0.9434573356363498,"citer_contribution":9.293426730841958,"corpus_percentile":98.77775199195483,"corpus_rank":159,"citation_count":538,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9588,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2014-11-26","fair_score":64.375,"fair_percentile":78.58719646799118,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":19246,"name":"Andreas Prlić","orcid":"0000-0001-6346-6391","position":1,"is_corresponding":false},{"id":23495,"name":"Chunxiao Bi","orcid":null,"position":2,"is_corresponding":false},{"id":124,"name":"Wolfgang F. 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Burley","orcid":null,"position":14,"is_corresponding":false},{"id":23505,"name":"Cole Christie","orcid":null,"position":15,"is_corresponding":false},{"id":127,"name":"John Westbrook","orcid":"0000-0002-6686-5475","position":16,"is_corresponding":false},{"id":23506,"name":"S.K. Burley","orcid":"0000-0002-2487-9713","position":17,"is_corresponding":false},{"id":19244,"name":"Peter W. Rose","orcid":"0000-0001-9981-9750","position":0,"is_corresponding":true}],"reference_count":57,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"25428375","pmcid":"PMC4383988","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":77.5,"fair_a":80.0,"fair_i":50.0,"fair_r":50.0,"fair_zscore":0.811,"fair_rationale":{"fair_score":64.38,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":77.5,"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":0.75,"signal":null,"rationale":"The paper describes rich metadata (e.g., symmetry, BIRD, DrugBank, UniProt, Pfam, SCOP) but does not explicitly state that metadata are machine-readable or provided in standard formats like RDF or JSON-LD."}]},"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 clearly specifies multiple access protocols (FTP, RESTful web services, mobile apps) and provides URLs and tables for data download and programmatic access."}]},"I":{"name":"Interoperable","score":50.0,"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":1.0,"signal":null,"rationale":"The paper uses standard formats (mmCIF, PDB, InChI, SMILES), vocabularies (ATC, UniProt, Pfam), and identifiers (PDB IDs, DrugBank IDs, UniProt accession codes) throughout."}]},"R":{"name":"Reusable","score":50.0,"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":0.833,"signal":null,"rationale":"The paper includes a clear open-access license (CC BY 4.0), provides data files and web services for reuse, and describes reproducibility through validation reports and open-source software, but lacks an explicit data-availability statement for the paper's own derived data."}]}},"suggestions":["Explicitly state that metadata are provided in machine-readable formats (e.g., JSON, XML, RDF) to improve findability.","Add a formal data-availability statement for the paper's own derived annotations and software.","Include persistent identifiers (e.g., DOIs) for datasets and software versions to enhance reusability.","Provide a license for the software components (e.g., GitHub repositories) to clarify reuse terms.","Document the exact versioning and release cycle of the data files and web services for reproducibility."],"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":"2026-06-18T00:33:54.685118Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}