{"doi":"10.1093/nar/gkae1109","title":"MDRepo—an open data warehouse for community-contributed molecular dynamics simulations of proteins","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Molecular Dynamics (MD) simulation of biomolecules provides important insights into conformational changes and dynamic behavior, revealing critical information about folding and interactions with other molecules. The collection of simulations stored in computers across the world holds immense potential to serve as training data for future Machine Learning models that will transform the prediction of structure, dynamics, drug interactions, and more. Ideally, there should exist an open access repository that enables scientists to submit and store their MD simulations of proteins and protein-drug interactions, and to find, retrieve, analyze, and visualize simulations produced by others. However, despite the ubiquity of MD simulation in structural biology, no such repository exists; as a result, simulations are instead stored in scattered locations without uniform metadata or access protocols. Here, we introduce MDRepo, a robust infrastructure that provides a relatively simple process for standardized community contribution of simulations, activates common downstream analyses on stored data, and enables search, retrieval, and visualization of contributed data. MDRepo is built on top of the open-source CyVerse research cyber-infrastructure, and is capable of storing petabytes of simulations, while providing high bandwidth upload and download capabilities and laying a foundation for cloud-based access to its stored data.</jats:p>","journal":"Nucleic Acids Research","year":2025,"id":588299,"datarank":0.5614807789288114,"base_score":2.772588722239781,"endowment":2.772588722239781,"self_citation_contribution":0.41588830833596724,"citation_network_contribution":0.14559247059284425,"self_endowment_contribution":0.41588830833596724,"citer_contribution":0.14559247059284425,"corpus_percentile":65.1,"corpus_rank":4509,"citation_count":15,"citer_count":12,"citers_with_citation_signal":7,"citers_with_endowment":7,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1505061,"name":"Ethan Ward","orcid":null,"position":1,"is_corresponding":false},{"id":1505062,"name":"Illyoung Choi","orcid":null,"position":2,"is_corresponding":false},{"id":1505063,"name":"Michele Cosi","orcid":null,"position":3,"is_corresponding":false},{"id":1505064,"name":"Tony Edgin","orcid":null,"position":4,"is_corresponding":false},{"id":1505065,"name":"Travis S Hughes","orcid":null,"position":5,"is_corresponding":false},{"id":1505066,"name":"Md Shafayet Islam","orcid":null,"position":6,"is_corresponding":false},{"id":1505067,"name":"Asif M Khan","orcid":null,"position":7,"is_corresponding":false},{"id":1505068,"name":"Aakash Kolekar","orcid":null,"position":8,"is_corresponding":false},{"id":1262191,"name":"Mariah Rayl","orcid":"0000-0003-0248-9754","position":9,"is_corresponding":false},{"id":1479359,"name":"Isaac Robinson","orcid":"0009-0004-7075-6054","position":10,"is_corresponding":false},{"id":1505069,"name":"Paul Sarando","orcid":null,"position":11,"is_corresponding":false},{"id":1505070,"name":"Edwin Skidmore","orcid":null,"position":12,"is_corresponding":false},{"id":1505071,"name":"Tyson L Swetnam","orcid":null,"position":13,"is_corresponding":false},{"id":1505072,"name":"Mariah Wall","orcid":null,"position":14,"is_corresponding":false},{"id":1505073,"name":"Zhuoyun Xu","orcid":"0000-0002-6322-3012","position":15,"is_corresponding":false},{"id":1505074,"name":"Michelle L Yung","orcid":null,"position":16,"is_corresponding":false},{"id":1491820,"name":"Nirav Merchant","orcid":"0000-0002-1988-8180","position":17,"is_corresponding":false},{"id":264756,"name":"Travis J. Wheeler","orcid":"0000-0003-2004-1785","position":18,"is_corresponding":false},{"id":826440,"name":"Amitava Roy","orcid":"0000-0002-9100-4108","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"MDRepo-an open data warehouse for community-contributed molecular dynamics simulations of proteins.","abstract":"Molecular Dynamics (MD) simulation of biomolecules provides important insights into conformational changes and dynamic behavior, revealing critical information about folding and interactions with other molecules. The collection of simulations stored in computers across the world holds immense potential to serve as training data for future Machine Learning models that will transform the prediction of structure, dynamics, drug interactions, and more. Ideally, there should exist an open access repository that enables scientists to submit and store their MD simulations of proteins and protein-drug interactions, and to find, retrieve, analyze, and visualize simulations produced by others. However, despite the ubiquity of MD simulation in structural biology, no such repository exists; as a result, simulations are instead stored in scattered locations without uniform metadata or access protocols. Here, we introduce MDRepo, a robust infrastructure that provides a relatively simple process for standardized community contribution of simulations, activates common downstream analyses on stored data, and enables search, retrieval, and visualization of contributed data. MDRepo is built on top of the open-source CyVerse research cyber-infrastructure, and is capable of storing petabytes of simulations, while providing high bandwidth upload and download capabilities and laying a foundation for cloud-based access to its stored data.","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"39535038","pmcid":"PMC11701643","openalex_id":null,"authors":[],"funders":[{"funder_name":"National Science Foundation","grant_id":"0735191","title":"PSCIC Full Proposal: The iPlant Collaborative: A Cyberinfrastructure-Centered Community for a New Plant Biology"},{"funder_name":"University of Arizona Research, Innovation &amp; Impact","grant_id":"BIO5","title":null},{"funder_name":"National Science Foundation","grant_id":"1265383","title":"The iPlant Collaborative: Cyberinfrastructure for the Life Sciences"},{"funder_name":"OAC","grant_id":"2137603","title":"Track 4:  Advanced CI Coordination Ecosystem: Monitoring and Measurement Services"},{"funder_name":"NSF IRES","grant_id":"1953405","title":"IRES Track II: Cross-disciplinary Computational Biology Training"},{"funder_name":"National Science Foundation","grant_id":"1743442","title":"CyVerse:   Cyberinfrastructure for the Life Sciences"},{"funder_name":"University of Arizona Research, Innovation &amp; Impact","grant_id":"IT4IR TRIF","title":null},{"funder_name":"OAC","grant_id":"2138286","title":"Track 2: Customized Multi-tier Assistance, Training, and Computational Help (MATCH) for End User ACCESS to CI"},{"funder_name":"OAC","grant_id":"2138307","title":"Track 3: COre National Ecosystem for CyberinfrasTructure (CONECT)"},{"funder_name":"Indiana University","grant_id":"BIO230080","title":null},{"funder_name":"OAC","grant_id":"2138259","title":"Track 1: ACCESS Resource Allocations Marketplace and Platform Services (RAMPS)"},{"funder_name":"OAC","grant_id":"2138296","title":"ACO: An Open CI Ecosystem to Advance Scientific Discovery (OpenCI)"}],"total_grants":12,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://doi.org/10.1093/nar/gkae1109","host_type":"publisher"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11701643/pdf/gkae1109.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC11701643","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC11701643?pdf=render","host_type":"Europe_PMC"},{"url":"https://pubmed.ncbi.nlm.nih.gov/39535038","host_type":""},{"url":"http://dx.doi.org/10.1093/nar/gkae1109","host_type":""}],"fields_of_study":["0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":["Proteins","Protein Conformation","Software","Databases, Protein","Molecular Dynamics Simulation"],"keywords":["Protein Conformation","Database Issue","Proteins","Molecular Dynamics Simulation","Databases, Protein","Software"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-20T06:14:17.148484Z","pmid":null,"pmcid":null,"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":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}