RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models is a dataset published in Nucleic Acids Research (2025). On theSindex it has a DataRank of 0.483, placing it in the top 39.5% of the data-sharing corpus. It has been cited 17 times, with 17 citing works in its 1-hop citation network. Its calibrated FAIR score is 4/100.
Ranks in the top 40% for downstream scientific impact
Linked data & code
DataRank reads this dataset's downstream impact straight off the citation graph — no black box, no proprietary weighting. How is this computed?
FAIR checklist signals are shown for context only and do not affect DataRank scoring.
Full FAIR picture · advisory
The headline score is computed from the scored criteria — the fact-shaped checks (a repository, an accession, a licence) that two independent models agree on. The advisory criteria below are real FAIR guidance but rest on judgment calls that models read differently, so they inform without moving the number.
The paper does not assign a persistent identifier (DOI, Handle, etc.) to the RCSB PDB dataset itself; it only mentions PDB accession codes for individual structures.
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'
The paper names the RCSB PDB as a repository, but it does so as the subject of the paper, not as the holder of a dataset generated by this study; no repository is named for the study's own data. [majority verdict 'no' (3/5 passes agreed)]
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
The dataset (RCSB PDB) does not appear as a reference-list entry; it is mentioned only in the body text and data availability statement. [downgraded to 'no' — no verifiable quote from the paper]
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'
Advisory · not in the published score
“The RCSB Protein Data Bank (PDB) is available at RCSB.org.”— not found in the paper; verdict downgraded
The data-availability statement points to a public repository (RCSB PDB) at a URL, which is a link to archived data in a public repository (Colavizza category 3). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]
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
The paper describes the repository's features and capabilities but does not provide an itemized inventory of the dataset's files, records, or variables.
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'
The paper does not provide an access route for its own data because it does not generate a dataset; the data availability statement points to the RCSB PDB repository, which is the subject of the paper, not a dataset from this study. [majority verdict 'no' (3/5 passes agreed)]
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'
Advisory · not in the published score
“All single-method experimental structures and integrative structures released in the archive are immediately accessible via the API services and RCSB.org.”— not found in the paper; verdict downgraded
The paper describes an access action (immediate accessibility) but does not apply an explicit access-level label such as 'open access' or 'freely available'. [downgraded to 'no' — no verifiable quote from the paper]
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
The data are not sensitive or human-subject; no gatekeeper is named.
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
The paper states that the data are updated weekly and immediately accessible, but makes no persistence commitment about how long they remain available.
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'
The paper mentions mmCIF and BinaryCIF formats used by the PDB, but these are not formats for a dataset generated by this study. [majority verdict 'no' (3/5 passes agreed)]
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
Advisory · not in the published score
The paper mentions community standards (e.g., IHMCIF) but these are applied to the PDB archive, not to a dataset from this study; the study itself does not produce data that conforms to a named standard. [majority verdict 'no' (3/5 passes agreed)]
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'
“Input experimental datasets used for modeling, together with links to related data in EMDB, PRIDE, and other repositories... including Biological Magnetic Resonance Data Bank (BMRB), Electron Microscopy Data Bank (EMDB), Small-angle Scattering Biological Data Bank (SASBDB), and PRoteomics IDEntifications Database (PRIDE).”— not found in the paper; verdict downgraded
The paper provides identifiers (names) of external resources that the data depend on, such as BMRB, EMDB, SASBDB, and PRIDE. [downgraded to 'no' — no verifiable quote from the paper]
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'
The paper states a CC BY license for the article itself, but does not state a license for the data.
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'
The paper says the repository is updated weekly but does not provide a version token or date for the dataset snapshot.
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'
The paper does not provide a locator for code generated by this study; it describes the RCSB.org website and APIs but not the study's own code.
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)
“RCSB PDB core operations are jointly funded by National Science Foundation (NSF) (DBI-2321666, PI: S.K. Burley), the US Department of Energy (DE-SC0019749, PI: S.K. Burley), and the National Cancer Institute, the National Institute of Allergy and Infectious Diseases, and the National Institute of General Medical Sciences of the NIH (R01GM157729, PI: S.K. Burley).”
The paper provides specific grant numbers (DBI-2321666, DE-SC0019749, R01GM157729) attached to named funders.
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
Advisory · not in the published score
The paper describes methods for the PDB-IHM pipeline, but not for the production of a dataset from this study; the study does not generate data with named instruments or software. [majority verdict 'no' (4/5 passes agreed)]
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
The paper does not mention any README, data dictionary, or codebook that accompanies the data.
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
Calibrated FAIR score — a parallel quality metric, independent of the DataRank citation score. See the full evaluation →
Base Score Contribution
0.434
From this paper's citation signal
Citation Network Contribution
0.0496
From 2 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 17 citers.
NSF
Grant: DBI-2321666
Department of Energy
Grant: DE-SC0019749
National Institute of General Medical Sciences
Grant: R01GM157729
NSF
Grant: DBI-2112966
National Institutes of Health
Grant: DBI-2112967
National Institutes of Health
Grant: R01GM083960
National Institutes of Health
Grant: P41GM109824
National Cancer Institute
National Institute of Allergy and Infectious Diseases
NCI NIH HHS
National Science Foundation
National Institute of Allergy and Infectious Diseases
NCI NIH HHS
National Science Foundation
FWCI
4.90
Citation Percentile
1.0%
Citation Trend
Fields of Study
MeSH Terms
Keywords