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PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

Pilot corpus: NIH-funded biomedical datasets. Any DOI can be scored on demand — network effects sharpen as coverage grows.

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

Journal of Molecular Biology(2022)10.1016/j.jmb.2022.167599Source: DataRank Database

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology is a dataset published in Journal of Molecular Biology (2022). On theSindex it has a DataRank of 2.1, placing it in the top 9.9% of the data-sharing corpus. It has been cited 95 times, with 55 citing works in its 1-hop citation network.

Top 10%percentile

2.1DataRank

Ranks in the top 10% for downstream scientific impact

Data paper Open Access95 citations · 55 citing works in its network

Cite:

DataRank reads this dataset's downstream impact straight off the citation graph — no black box, no proprietary weighting. How is this computed?

›Methodology & internals

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Pipeline:MetadataData-paper checkEnrichmentCitation networkScoring

Enrichment:Funding (16 grants)Impact (FWCI 5.96)OA: hybridTopics (27)IDs (PubMed, OpenAlex)

FAIR Checklist

Context only (not used in score)

FFindable (1/2)

Has DOI

AAccessible (1/2)

Open Access

IInteroperable (0/2)

RReusable (1/3)

Dataset classification

FAIR checklist signals are shown for context only and do not affect DataRank scoring.

Run a calibrated FAIR evaluation for this paper →

We only score data papers we can read in full — never from an abstract alone.

DataRank Breakdown

Base Score 32%Citation Network 68%

Base Score Contribution

0.685

From this paper's citation signal

Citation Network Contribution

1.5

From 38 citing papers with measurable signal

Learn more about DataRank methodology →

Top 5 citers driving the network score

Ranked by each citer's contribution to N(p) — log1p(C_q) divided by its reference count — out of 55 citers.

Foldcomp: a library and format for compressing and indexing large protein structure sets
Bioinformatics202330 citations15 referencesContributes 0.229
The curse of the protein ribbon diagram
PLoS Biology20227 citations13 referencesContributes 0.160
Efficient protein structure archiving using ProteStAr
Bioinformatics20244 citations15 referencesContributes 0.107
AlphaPulldown2—a general pipeline for high-throughput structural modeling
Bioinformatics202516 citations31 referencesContributes 0.091
The structure assessment web server: for proteins, complexes and more
Nucleic Acids Research2024123 citations54 referencesContributes 0.089

Authors (22)

Jasmine Young ORCID,Chenghua Shao ORCID,Zukang Feng ORCID,Vladimir Guranović ORCID,Catherine L. Lawson ORCID

Live enrichment

PubMed:35460671 OpenAlex:https://openalex.org/W4224303521

European Commission

Grant: 284209

National Science Foundation

Grant: DBI-1832184

National Science Foundation

Grant: DBI-2019297

Wellcome Trust

Grant: 104948

Biotechnology and Biological Sciences Research Council

Grant: BB/G022577/1

Biotechnology and Biological Sciences Research Council

Grant: BB/J007471/1

Biotechnology and Biological Sciences Research Council

Grant: BB/K016970/1

Biotechnology and Biological Sciences Research Council

Grant: BB/K020013/1

Biotechnology and Biological Sciences Research Council

Grant: BB/M011674/1

Biotechnology and Biological Sciences Research Council

Grant: BB/M013146/1

Biotechnology and Biological Sciences Research Council

Grant: BB/M020347/1

Biotechnology and Biological Sciences Research Council

Grant: BB/M020428/1

Biotechnology and Biological Sciences Research Council

Grant: BB/N019172/1

Biotechnology and Biological Sciences Research Council

Grant: BB/P024351/1

National Institute of General Medical Sciences

Grant: R01GM133198

U.S. Department of Energy

Grant: DE-SC0019749

FWCI

5.96

Citation Percentile

1.0%

Citation Trend

2013

2022

2023

2024

2025

2026

hybridLicense: cc-by

journalhttps://linkinghub.elsevier.com/retrieve/pii/S0022283622001796

publisherhttps://linkinghub.elsevier.com/retrieve/pii/S0022283622001796

publisherhttps://api.elsevier.com/content/article/PII:S0022283622001796?httpAccept=text/xml

publisherhttps://api.elsevier.com/content/article/PII:S0022283622001796?httpAccept=text/plain

journalhttps://doi.org/10.1016/j.jmb.2022.167599

Fields of Study

Enzyme Structure and FunctionProtein Structure and DynamicsGenomics and Phylogenetic Studies

MeSH Terms

CrystallographyMolecular BiologyProtein ConformationSemanticsSoftwareComputational BiologyDatabases, ProteinMacromolecular Substances

Keywords

Protein Data BankComputer scienceSoftwareProtein Data Bank (RCSB PDB)Data scienceData bankBiological dataExternal Data RepresentationOpen dataInformation retrievalWorld Wide WebBioinformaticsBiologyArtificial intelligenceProtein structureProgramming language

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