{"doi":"10.1093/nar/gkab119","title":"<i>De novo</i>3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures","abstract":"The rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosetta's FARFAR2 algorithm for SARS-CoV-2 RNA regions including the individual stems SL1-8 in the extended 5' UTR; the reverse complement of the 5' UTR SL1-4; the frameshift stimulating element (FSE); and the extended pseudoknot, hypervariable region, and s2m of the 3' UTR. For eleven of these elements (the stems in SL1-8, reverse complement of SL1-4, FSE, s2m and 3' UTR pseudoknot), modeling convergence supports the accuracy of predicted low energy states; subsequent cryo-EM characterization of the FSE confirms modeling accuracy. To aid efforts to discover small molecule RNA binders guided by computational models, we provide a second set of similarly prepared models for RNA riboswitches that bind small molecules. Both datasets ('FARFAR2-SARS-CoV-2', https://github.com/DasLab/FARFAR2-SARS-CoV-2; and 'FARFAR2-Apo-Riboswitch', at https://github.com/DasLab/FARFAR2-Apo-Riboswitch') include up to 400 models for each RNA element, which may facilitate drug discovery approaches targeting dynamic ensembles of RNA molecules.","journal":"Nucleic Acids Research","year":2021,"id":151140,"datarank":2.8222485521618763,"base_score":4.454347296253507,"endowment":4.454347296253507,"self_citation_contribution":0.6681520944380261,"citation_network_contribution":2.1540964577238504,"self_endowment_contribution":0.6681520944380261,"citer_contribution":2.1540964577238504,"corpus_percentile":92.2487816198654,"corpus_rank":1003,"citation_count":85,"citer_count":81,"citers_with_citation_signal":72,"citers_with_endowment":72,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7713,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":58.3333,"fair_percentile":72.8829104249465,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":58890,"name":"Andrew M. Watkins","orcid":"0000-0003-1617-1720","position":1,"is_corresponding":false},{"id":554162,"name":"Jose Chacon","orcid":"0000-0001-7965-3976","position":2,"is_corresponding":false},{"id":232524,"name":"Rachael C. Kretsch","orcid":"0000-0002-6935-518X","position":3,"is_corresponding":false},{"id":252521,"name":"Wipapat Kladwang","orcid":null,"position":4,"is_corresponding":false},{"id":235779,"name":"Ivan N. Zheludev","orcid":"0000-0002-9572-0574","position":5,"is_corresponding":false},{"id":554163,"name":"Jill Townley","orcid":"0000-0001-8528-2227","position":6,"is_corresponding":false},{"id":492053,"name":"Mats Rynge","orcid":"0000-0002-1779-7189","position":7,"is_corresponding":false},{"id":554164,"name":"Greg Thain","orcid":"0000-0002-2296-3735","position":8,"is_corresponding":false},{"id":235783,"name":"Rhiju Das","orcid":"0000-0001-7497-0972","position":9,"is_corresponding":false},{"id":235778,"name":"Ramya Rangan","orcid":"0000-0002-0960-0825","position":0,"is_corresponding":true}],"reference_count":66,"raw_metadata":null,"created_at":"2026-07-18T23:43:11.293086Z","pmid":"33693814","pmcid":"PMC8034642","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":94.4444,"fair_a":62.5,"fair_i":0.0,"fair_r":33.3333,"fair_zscore":0.9454,"fair_rationale":{"fair_score":58.33,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":94.44,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab).","grounded":true,"rationale":"The paper provides RMDB accession numbers for the chemical probing data, which are persistent identifiers issued by a curated repository. [majority verdict 'yes' (3/5 passes agreed)]","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":1.0,"verdict":"yes","evidence":"Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab).","grounded":true,"rationale":"RMDB is named as the repository for chemical probing data; RMDB is a data repository listed in re3data, fulfilling the 'yes' class. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The supplementary file includes depictions of top-scoring cluster centers for the full extended 5′ UTR, the extended FSE with alternative secondary structures, the FSE dimer, the full 3′ UTR, the hypervariable region and an extended 3′ UTR pseudoknot construct modeled with both the BSL and extended pseudoknot secondary structures. Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab). FARFAR2-SARS-CoV-2 models are included at https://github.com/DasLab/FARFAR2-SARS-CoV-2 . FARFAR2-Apo-Riboswitch models are included at https://github.com/DasLab/FARFAR2-Apo-Riboswitch . Pocket predictions are included in the Github repositories. Large model sets, comprising the top 5% of models for each simulation as ranked by Rosetta score, are included at the PURL repository https://purl.stanford.edu/pp620tj8748 .","grounded":true,"rationale":"The data availability statement points to multiple public repositories (RMDB, GitHub, PURL) with accessions and URLs, corresponding to Colavizza category 3 (link to archived data in a public repository).","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Table 1. FARFAR2-SARS-CoV-2 models","grounded":true,"rationale":"The paper includes a structured table (Table 1) that lists the modeled systems, lengths, and generation metrics, providing an itemised inventory of the dataset.","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab).","grounded":true,"rationale":"The dataset identifiers (RMDB accessions, GitHub URLs, PURL) appear only in the body text (Data Availability section) and not as a reference-list entry.","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":62.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab).","grounded":true,"rationale":"The data availability statement gives URLs to RMDB, GitHub, and a PURL without any precondition such as embargo, registration, or application; the data are stated to be available now.","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab).","grounded":true,"rationale":"The paper states the data are available on RMDB and GitHub, which describes the access action but does not apply an explicit access-level label such as 'open access' or 'freely available'. [majority verdict 'partial' (3/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are not sensitive human-subject data, and no gatekeeper is named; the criterion is not applicable, so the verdict is 'no'.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not mention any retention period, persistence commitment, or timing of availability beyond the current availability statement.","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":0.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not name any file format (open or proprietary) for the released data; only the term 'models' is used without specifying a format token.","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No data or metadata community standard (e.g., MIAME, FAIRsharing-registered ontology) is named for the data; only manuscript reporting guidelines are absent.","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"For the 5′ UTR SL2, PDB ID 2L6I (11) was used as a template for positions 45–59.","grounded":false,"rationale":"The paper cites PDB IDs (2L6I, 1XJR) for external structural templates used in homology modeling. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":33.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No license or terms-of-use document is named for the data; the CC-BY license applies only to the article, not the data.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"The models were created using the rna_denovo application in Rosetta 3.12 using default parameters for FARFAR2","grounded":true,"rationale":"The paper names specific software (Rosetta 3.12, FARFAR2) and instruments (Miseq, T7 TranscriptAid kits) used to produce the data, fulfilling the 'yes' class.","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The supplementary file includes depictions of top-scoring cluster centers for the full extended 5′ UTR, the extended FSE with alternative secondary structures, the FSE dimer, the full 3′ UTR, the hypervariable region and an extended 3′ UTR pseudoknot construct modeled with both the BSL and extended pseudoknot secondary structures.","grounded":true,"rationale":"Variable-level definitions are provided within the article (supplementary file) rather than in a separate documentation object shipped with the data. [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"Neither a version token nor a date is provided to identify which snapshot of the data was released; the data are referred to without versioning.","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not provide a locator for the study's own code; it only mentions third-party software (HiTRACE, Biers, Rosetta) without offering the custom scripts used. [majority verdict 'no' (4/5 passes agreed)]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"National Institutes of Health [R21 AI145647, R35 GM122579]","grounded":true,"rationale":"The paper includes award/grant numbers (e.g., NIH R21 AI145647, R35 GM122579) attached to named funders, meeting the 'yes' class.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No license or terms-of-use document is named for the data; the CC-BY license applies only to the article, not the data.","gain":16.67,"priority":"essential","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open structural biology formats such as mmCIF or MTZ.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not name any file format (open or proprietary) for the released data; only the term 'models' is used without specifying a format token.","gain":8.33,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not provide a locator for the study's own code; it only mentions third-party software (HiTRACE, Biers, Rosetta) without offering the custom scripts used. [majority verdict 'no' (4/5 passes agreed)]","gain":8.33,"priority":"important","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the structural biology repository accession (e.g. from the Protein Data Bank (PDB) or EMDB) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab).","why":"The dataset identifiers (RMDB accessions, GitHub URLs, PURL) appear only in the body text (Data Availability section) and not as a reference-list entry.","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"Neither a version token nor a date is provided to identify which snapshot of the data was released; the data are referred to without versioning.","gain":4.17,"priority":"useful","scored":true},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab).","why":"The paper states the data are available on RMDB and GitHub, which describes the access action but does not apply an explicit access-level label such as 'open access' or 'freely available'. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In structural biology, describe the data with mmCIF/PDBx.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No data or metadata community standard (e.g., MIAME, FAIRsharing-registered ontology) is named for the data; only manuscript reporting guidelines are absent.","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The supplementary file includes depictions of top-scoring cluster centers for the full extended 5′ UTR, the extended FSE with alternative secondary structures, the FSE dimer, the full 3′ UTR, the hypervariable region and an extended 3′ UTR pseudoknot construct modeled with both the BSL and extended pseudoknot secondary structures.","why":"Variable-level definitions are provided within the article (supplementary file) rather than in a separate documentation object shipped with the data. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are not sensitive human-subject data, and no gatekeeper is named; the criterion is not applicable, so the verdict is 'no'.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"For the 5′ UTR SL2, PDB ID 2L6I (11) was used as a template for positions 45–59.","why":"The paper cites PDB IDs (2L6I, 1XJR) for external structural templates used in homology modeling. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not mention any retention period, persistence commitment, or timing of availability beyond the current availability statement.","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open structural biology formats such as mmCIF or MTZ.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the structural biology repository accession (e.g. from the Protein Data Bank (PDB) or EMDB) in the reference list.","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:08:05.293830Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}