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MDRepo—an open data warehouse for community-contributed molecular dynamics simulations of proteins

Name: MDRepo—an open data warehouse for community-contributed molecular dynamics simulations of proteins
Published: 2025

Nucleic Acids Research(2025)10.1093/nar/gkae1109Source: DataRank Database

MDRepo—an open data warehouse for community-contributed molecular dynamics simulations of proteins is a dataset published in Nucleic Acids Research (2025). On theSindex it has a DataRank of 0.561, placing it in the top 34.9% of the data-sharing corpus. It has been cited 15 times, with 12 citing works in its 1-hop citation network.

Top 35%percentile

0.561DataRank

Ranks in the top 35% for downstream scientific impact

Data paper15 citations · 12 citing works in its network

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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 (12 grants)Impact (FWCI 2.62)OA: goldTopics (26)IDs (PubMed, PMC, OpenAlex)SDGs (1)

FAIR Checklist

Context only (not used in score)

Findable (1/2)

Has DOI

Accessible (0/2)

Interoperable (0/2)

Reusable (1/3)

Dataset classification

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DataRank Breakdown

Base Score 74%Citation Network 26%

Base Score Contribution

0.416

From this paper's citation signal

Citation Network Contribution

0.146

From 7 citing papers with measurable signal

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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 12 citers.

Gromacs MetaDump: a tool for extracting GROMACS simulation metadata
Journal of Cheminformatics20251 citations16 referencesContributes 0.043
DynaRepo: the repository of macromolecular conformational dynamics
Nucleic Acids Research20258 citations54 referencesContributes 0.041
Recent advances in computational strategies for allosteric site prediction: Machine learning, molecular dynamics, and network-based approaches
Drug Discovery Today202511 citations95 referencesContributes 0.026
DynaRepo: The repository of macromolecular conformational dynamics
bioRxiv (Cold Spring Harbor Laboratory)20252 citations44 referencesContributes 0.025
A FAIR-Compliant Management Solution for Molecular Simulation Trajectories
Journal of Chemical Information and Modeling20253 citations69 referencesContributes 0.020

Authors (19)

Ethan Ward,Illyoung Choi,Michele Cosi,Tony Edgin,Travis S Hughes

Live enrichment

PubMed:39535038 PMC:PMC11701643 OpenAlex:https://openalex.org/W4404328867

National Science Foundation

Grant: 0735191

PSCIC Full Proposal: The iPlant Collaborative: A Cyberinfrastructure-Centered Community for a New Plant Biology

National Science Foundation

Grant: 1265383

The iPlant Collaborative: Cyberinfrastructure for the Life Sciences

National Science Foundation

Grant: 1743442

CyVerse: Cyberinfrastructure for the Life Sciences

University of Arizona Research, Innovation & Impact

Grant: BIO5

University of Arizona Research, Innovation & Impact

Grant: IT4IR TRIF

Indiana University

Grant: BIO230080

OAC

Grant: 2138259

Track 1: ACCESS Resource Allocations Marketplace and Platform Services (RAMPS)

OAC

Grant: 2138286

Track 2: Customized Multi-tier Assistance, Training, and Computational Help (MATCH) for End User ACCESS to CI

OAC

Grant: 2138307

Track 3: COre National Ecosystem for CyberinfrasTructure (CONECT)

OAC

Grant: 2137603

Track 4: Advanced CI Coordination Ecosystem: Monitoring and Measurement Services

OAC

Grant: 2138296

ACO: An Open CI Ecosystem to Advance Scientific Discovery (OpenCI)

NSF IRES

Grant: 1953405

IRES Track II: Cross-disciplinary Computational Biology Training

FWCI

2.62

Citation Percentile

0.9%

Citation Trend

2025

2026

goldLicense: cc-by

journalhttps://doi.org/10.1093/nar/gkae1109

publisherhttps://doi.org/10.1093/nar/gkae1109

publisherhttps://academic.oup.com/nar/article-pdf/53/D1/D477/60645348/gkae1109.pdf

repositoryhttps://pubmed.ncbi.nlm.nih.gov/39535038

repositoryhttps://www.ncbi.nlm.nih.gov/pmc/articles/11701643

Fields of Study

Bioinformatics and Genomic NetworksMicrobial Metabolic Engineering and BioproductionProtein Structure and Dynamics0301 basic medicine0303 health sciences03 medical and health sciences

MeSH Terms

Protein ConformationProteinsSoftwareDatabases, ProteinMolecular Dynamics Simulation

Keywords

BiologyComputational biologyDynamics (music)Data warehouseData scienceGeneticsEvolutionary biologyDatabaseComputer scienceProtein ConformationDatabase IssueProteinsMolecular Dynamics SimulationDatabases, ProteinSoftware

Sustainable Development Goals

SDG 0: Industry, innovation and infrastructure