BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data is a dataset published in Nucleic Acids Research (2024). On theSindex it has a DataRank of 2.0, placing it in the top 10.6% of the data-sharing corpus. It has been cited 187 times, with 100 citing works in its 1-hop citation network. Its calibrated FAIR score is 85/100.
Ranks in the top 11% 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.
“BindingDB cuts a new archival version, which includes detailed metadata, on a quarterly basis ( https://doi.org/10.6075/J0HD7VVF ).”
The paper provides a DOI for the archival version of the dataset. [majority verdict 'yes' (3/5 passes agreed)]
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'
“BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins”
The paper names BindingDB as the holder of the data, which is a public database and a FAIRsharing resource.
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
“BindingDB cuts a new archival version, which includes detailed metadata, on a quarterly basis (https://doi.org/10.6075/J0HD7VVF)”— not found in the paper; verdict downgraded
The dataset DOI appears in the body text but not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]
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
“Data curated by BindingDB are shared under the Creative Commons Attribution 4.0 License (https://creativecommons.org/licenses/by/4.0 )”— not found in the paper; verdict downgraded
The statement points to a license, not a repository record, and does not provide a direct link to the data. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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 BindingDB dataset”
The paper includes a dedicated section heading that describes the dataset structure and content. [majority verdict 'yes' (3/5 passes agreed)]
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'
“BindingDB provides open access to a growing dataset”
The paper states the data are openly available at the repository with no stated precondition. [majority verdict 'yes' (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
“BindingDB provides open access to a growing dataset”
The paper explicitly labels the data as 'open access' in the abstract. [majority verdict 'yes' (4/5 passes agreed)]
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
“BindingDB provides open access to a growing dataset”
The data are not sensitive or human-subject; no gatekeeper is named and access is open.
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
“Long-term Archiving of BindingDB Data : A long-term, open-access, archive of BindingDB data has been established within the UC San Diego Library Research Data Collections.”
The paper commits to long-term preservation of the data. [majority verdict 'yes' (4/5 passes agreed)]
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'
“a tab-separated value (TSV) file with SMILES and InChI strings as well as SDfiles with 2D or computed 3D structures, is available for immediate download”— not found in the paper; verdict downgraded
TSV is an open, non-proprietary format. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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
No FAIRsharing-registered data or metadata community standard is named; SMILES and InChI are not on the list. [majority verdict 'no' (2/5 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'
“the UniProt ID of the target”
The paper mentions identifiers for external resources (UniProt IDs, PubChem IDs) that the data reference. [majority verdict 'yes' (3/5 passes agreed)]
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'
“Data curated by BindingDB are shared under the Creative Commons Attribution 4.0 License (CC BY 4.0).”
An open standard license (CC BY 4.0) is explicitly stated 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'
“BindingDB cuts a new archival version, which includes detailed metadata, on a quarterly basis (https://doi.org/10.6075/J0HD7VVF).”— not found in the paper; verdict downgraded
The DOI for the archive is a version-specific identifier. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]
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'
“https://colab.research.google.com/github/PatWalters/practical_cheminformatics_tutorials/blob/main/patent/patent_analysis.ipynb”
A machine-resolvable URL to a GitHub-hosted notebook is provided, qualifying as a code repository location. [majority verdict 'yes' (4/5 passes agreed)]
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)
“National Institute of General Medical Sciences of the National Institutes of Health [R24GM144232]”
Award numbers are given for the funding sources. [majority verdict 'yes' (4/5 passes agreed)]
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
“We then use purpose-built software to identify patents likely to contain suitable data.”
The description of data production is generic and does not name specific instruments, kits, or software versions. [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 BindingDB dataset”
Variable and file definitions are provided within the article text, but no separate documentation object is named as accompanying 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
0.785
From this paper's citation signal
Citation Network Contribution
1.2
From 69 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 100 citers.
National Institute of General Medical Sciences
Grant: R24GM144232
National Institute of General Medical Sciences
Grant: R01GM157729
National Science Foundation
Grant: DBI-2321666
Department of Energy
Grant: DE-SC0019749
National Institutes of Health
Grant: 1F31DE019749-01A1
Dysregulation of microRNAs in HPV-Positive Oropharyngeal Cancers
National Science Foundation
Grant: 2321666
PDB Management by The Research Collaboratory for Structural Bioinformatics
National Institutes of Health
Grant: 5R01GM157729-02
PDB Management by the Research Collaboratory for Structural Bioinformatics
National Institutes of Health
Grant: 5R24GM144232-02
BindingDB: An Open Knowledgebase of Protein-Small Molecule Interactions
National Institutes of Health
Grant: 5R01GM133198-02
PDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICS
NIH HHS
National Institute of Allergy and Infectious Diseases
National Cancer Institute
National Institutes of Health
NCI NIH HHS
Fields of Study
MeSH Terms
Keywords