{"doi":"10.1093/nar/gkad630","title":"BioLiP2: an updated structure database for biologically relevant ligand–protein interactions","abstract":"With the progress of structural biology, the Protein Data Bank (PDB) has witnessed rapid accumulation of experimentally solved protein structures. Since many structures are determined with purification and crystallization additives that are unrelated to a protein's in vivo function, it is nontrivial to identify the subset of protein-ligand interactions that are biologically relevant. We developed the BioLiP2 database (https://zhanggroup.org/BioLiP) to extract biologically relevant protein-ligand interactions from the PDB database. BioLiP2 assesses the functional relevance of the ligands by geometric rules and experimental literature validations. The ligand binding information is further enriched with other function annotations, including Enzyme Commission numbers, Gene Ontology terms, catalytic sites, and binding affinities collected from other databases and a manual literature survey. Compared to its predecessor BioLiP, BioLiP2 offers significantly greater coverage of nucleic acid-protein interactions, and interactions involving large complexes that are unavailable in PDB format. BioLiP2 also integrates cutting-edge structural alignment algorithms with state-of-the-art structure prediction techniques, which for the first time enables composite protein structure and sequence-based searching and significantly enhances the usefulness of the database in structure-based function annotations. With these new developments, BioLiP2 will continue to be an important and comprehensive database for docking, virtual screening, and structure-based protein function analyses.","journal":"Nucleic Acids Research","year":2023,"id":315710,"datarank":2.979883141253782,"base_score":4.948759890378168,"endowment":4.948759890378168,"self_citation_contribution":0.7423139835567254,"citation_network_contribution":2.2375691576970564,"self_endowment_contribution":0.7423139835567254,"citer_contribution":2.2375691576970564,"corpus_percentile":92.5736829890926,"corpus_rank":961,"citation_count":140,"citer_count":100,"citers_with_citation_signal":92,"citers_with_endowment":92,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9419,"is_data_producer":true,"deposit_databanks":{"figshare":["23641701"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":66.6667,"fair_percentile":86.48731274839498,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":506457,"name":"Xi Zhang","orcid":"0000-0002-8548-2832","position":1,"is_corresponding":false},{"id":506370,"name":"Lydia Freddolino","orcid":"0000-0002-5821-4226","position":2,"is_corresponding":false},{"id":287631,"name":"Yang Zhang","orcid":"0000-0002-2739-1916","position":3,"is_corresponding":false},{"id":121996,"name":"Chengxin Zhang","orcid":"0000-0001-7290-1324","position":0,"is_corresponding":true}],"reference_count":53,"raw_metadata":null,"created_at":"2026-07-19T01:06:32.274501Z","pmid":"37522378","pmcid":"PMC10767969","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":50.0,"fair_a":62.5,"fair_i":40.0,"fair_r":66.6667,"fair_zscore":1.2752,"fair_rationale":{"fair_score":66.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":50.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.","grounded":true,"rationale":"The database itself is given a web address (https://zhanggroup.org/BioLiP/), not a persistent identifier; the DOI is for the source code, not the dataset. [majority verdict 'partial' (4/5 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":0.5,"verdict":"partial","evidence":"The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.","grounded":true,"rationale":"The database is hosted on a lab website (zhanggroup.org), not a named data repository. [majority verdict 'partial' (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":0.5,"verdict":"partial","evidence":"The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.","grounded":true,"rationale":"The data-availability statement points to a lab website and a code repository, not to a repository record with an accession for the database itself. [majority verdict 'partial' (4/5 passes agreed)]","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":0.5,"verdict":"partial","evidence":"BioLiP2 contains 385 160 protein chains involved in 781 684 protein–ligand interactions, including 35 167 (4%), 36 784 (5%), 127 525 (33%), 174 257 (45%) and 40 7951 (52%) interactions with peptides, DNAs, RNAs, metal ions, and other small molecules (which are referred to as 'regular' ligands by BioLiP2), respectively.","grounded":true,"rationale":"The dataset's content is described in running prose, not in an itemised inventory (section, table, or enumerated list). [majority verdict 'partial' (4/5 passes agreed)]","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":"The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.","grounded":true,"rationale":"The dataset's identifier (the URL) appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (4/5 passes agreed)]","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":"The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.","grounded":true,"rationale":"The text gives a route to the data with no stated precondition; the database is stated to be available without any requirement to await, register, or apply. [majority verdict 'yes' (4/5 passes agreed)]","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":"The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.","grounded":true,"rationale":"The paper describes the access action of where the data can be obtained but does not label the access level with an explicit term from the controlled vocabulary. [majority verdict 'partial' (4/5 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 or human-subject, so no gatekeeper is named.","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 state how long the data will remain available, nor does it make a persistence commitment. [majority verdict 'no' (3/5 passes agreed)]","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":40.0,"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":"No file format is named for the released data. [majority verdict 'no' (3/5 passes agreed)]","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":1.0,"verdict":"yes","evidence":"The ligand binding information is further enriched with other function annotations, including Enzyme Commission numbers, Gene Ontology terms, catalytic sites, and binding affinities collected from other databases and a manual literature survey.","grounded":true,"rationale":"The paper names community standards (GO terms, EC numbers) that are applied to the data. [majority verdict 'yes' (4/5 passes agreed)]","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":"BioLiP2 contains 3385 protein–ligand interactions from 812 protein chains extracted from mmCIF file of the phycobilisome structure (PDB 5y6p, https://zhanggroup.org/BioLiP/qsearch.cgi?&page=last&order=pdbid&pdbid=5y6p )","grounded":false,"rationale":"The paper provides identifiers (e.g., PDB ID 5y6p) for external resources used or referenced. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 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":66.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.","grounded":true,"rationale":"The BSD license is an open standard license named for the data. [majority verdict 'yes' (4/5 passes agreed)]","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":0.5,"verdict":"partial","evidence":"In the first step, the mmCIF files of all protein-containing structures are downloaded from the PDB database and split into chains by a modified version of the BeEM tool (43).","grounded":false,"rationale":"The paper names specific tools (BeEM, Foldseek, US-align, etc.) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","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":0.0,"verdict":"no","evidence":"The 'BROWSE' interface displays the PDB ID and chain ID, resolution, ligand, EC number, GO terms, UniProt accessions, PubMed citations and binding affinities, either for all protein–ligand interactions or for the subset of interactions with regular ligands, metal ions, RNAs, DNAs, and peptides (Figure 3A).","grounded":false,"rationale":"Variable-level definitions are described inside the article, but no documentation object is said to accompany the data. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":"No version token or date is given to identify a specific snapshot of the database. [majority verdict 'no' (3/5 passes agreed)]","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":1.0,"verdict":"yes","evidence":"The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.","grounded":true,"rationale":"A machine-resolvable locator (GitHub URL and figshare DOI) is given for the code. [majority verdict 'yes' (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 Institute of General Medical Sciences [GM136422 and S10OD026825 to Y.Z.]; National Institute of Allergy and Infectious Diseases [AI134678 to L.F. and Y.Z.]; National Science Foundation [IIS1901191 and DBI2030790 to Y.Z. and MTM2025426 to L.F. and Y.Z.].","grounded":true,"rationale":"Award numbers are attached to named funders. [majority verdict 'yes' (4/5 passes agreed)]","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":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For structural biology data, deposit in the Protein Data Bank (PDB) or EMDB.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.","why":"The database itself is given a web address (https://zhanggroup.org/BioLiP/), not a persistent identifier; the DOI is for the source code, not the dataset. [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For structural biology data, deposit in the Protein Data Bank (PDB) or EMDB.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.","why":"The database is hosted on a lab website (zhanggroup.org), not a named data repository. [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"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":"No file format is named for the released data. [majority verdict 'no' (3/5 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":"The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.","why":"The dataset's identifier (the URL) appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (4/5 passes agreed)]","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":"No version token or date is given to identify a specific snapshot of the database. [majority verdict 'no' (3/5 passes agreed)]","gain":4.17,"priority":"useful","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.","why":"The data-availability statement points to a lab website and a code repository, not to a repository record with an accession for the database itself. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"BioLiP2 contains 385 160 protein chains involved in 781 684 protein–ligand interactions, including 35 167 (4%), 36 784 (5%), 127 525 (33%), 174 257 (45%) and 40 7951 (52%) interactions with peptides, DNAs, RNAs, metal ions, and other small molecules (which are referred to as 'regular' ligands by BioLiP2), respectively.","why":"The dataset's content is described in running prose, not in an itemised inventory (section, table, or enumerated list). [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"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":"The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.","why":"The paper describes the access action of where the data can be obtained but does not label the access level with an explicit term from the controlled vocabulary. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"In the first step, the mmCIF files of all protein-containing structures are downloaded from the PDB database and split into chains by a modified version of the BeEM tool (43).","why":"The paper names specific tools (BeEM, Foldseek, US-align, etc.) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","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":"no","current":0.0,"evidence":"The 'BROWSE' interface displays the PDB ID and chain ID, resolution, ligand, EC number, GO terms, UniProt accessions, PubMed citations and binding affinities, either for all protein–ligand interactions or for the subset of interactions with regular ligands, metal ions, RNAs, DNAs, and peptides (Figure 3A).","why":"Variable-level definitions are described inside the article, but no documentation object is said to accompany the data. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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 or human-subject, so no gatekeeper is named.","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":"BioLiP2 contains 3385 protein–ligand interactions from 812 protein chains extracted from mmCIF file of the phycobilisome structure (PDB 5y6p, https://zhanggroup.org/BioLiP/qsearch.cgi?&page=last&order=pdbid&pdbid=5y6p )","why":"The paper provides identifiers (e.g., PDB ID 5y6p) for external resources used or referenced. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 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 state how long the data will remain available, nor does it make a persistence commitment. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For structural biology data, deposit in the Protein Data Bank (PDB) or EMDB.","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For structural biology data, deposit in the Protein Data Bank (PDB) or EMDB.","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.","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":"2026-07-20T10:59:28.618636Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}