{"doi":"10.1093/nar/gkad957","title":"The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids","abstract":"The Nucleic Acid Knowledgebase (nakb.org) is a new data resource, updated weekly, for experimentally determined 3D structures containing DNA and/or RNA nucleic acid polymers and their biological assemblies. NAKB indexes nucleic acid-containing structures derived from all major structure determination methods (X-ray, NMR and EM), including all held by the Protein Data Bank (PDB). As the planned successor to the Nucleic Acid Database (NDB), NAKB's design preserves all functionality of the NDB and provides novel nucleic acid-centric content, including structural and functional annotations, as well as annotations from and links to external resources. A variety of custom interactive tools have been developed to enable rapid exploration and drill-down of NAKB's content.","journal":"Nucleic Acids Research","year":2023,"id":318844,"datarank":1.585712551681186,"base_score":4.127134385045092,"endowment":4.127134385045092,"self_citation_contribution":0.6190701577567639,"citation_network_contribution":0.9666423939244221,"self_endowment_contribution":0.6190701577567639,"citer_contribution":0.9666423939244221,"corpus_percentile":86.9111162682757,"corpus_rank":1693,"citation_count":61,"citer_count":54,"citers_with_citation_signal":34,"citers_with_endowment":34,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9454,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":29.1667,"fair_percentile":43.01436869458881,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":2156,"name":"Helen M. Berman","orcid":"0000-0002-3337-0660","position":1,"is_corresponding":false},{"id":1026895,"name":"Li Chen","orcid":"0000-0002-8200-7681","position":2,"is_corresponding":false},{"id":623810,"name":"Brinda Vallat","orcid":"0000-0002-4076-8984","position":3,"is_corresponding":false},{"id":493596,"name":"Craig L. Zirbel","orcid":"0000-0002-3281-918X","position":4,"is_corresponding":false},{"id":469135,"name":"Catherine L. Lawson","orcid":"0000-0002-3261-7035","position":0,"is_corresponding":true}],"reference_count":50,"raw_metadata":null,"created_at":"2026-07-19T01:07:06.454099Z","pmid":"37953312","pmcid":"PMC10767938","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":11.1111,"fair_a":25.0,"fair_i":100.0,"fair_r":25.0,"fair_zscore":-0.2091,"fair_rationale":{"fair_score":29.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":11.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"nakb.org/download.html","grounded":true,"rationale":"The only identifier for the dataset is a web URL, not a persistent identifier scheme such as DOI, Handle, or repository accession.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"The Nucleic Acid Knowledgebase (nakb.org) is a new data resource","grounded":false,"rationale":"NAKB is a named host but is a custom database, not a repository listed in re3data/FAIRsharing with standard accessioning. 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