ArticleStructure (London, England : 1993)2017
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.
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Article in Structure (London, England : 1993), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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96citing papers in PubMed
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96 citing papers in PubMed.
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- The NMR Exchange Format (NEF): Specification and Applications.bioRxiv : the preprint server for biology · 2026Article
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- Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study.Protein science : a publication of the Protein Society · 2025Article
- Structural and biochemical analysis of ligand binding in yeast Niemann-Pick type C1-related protein.Life science alliance · 2025Article
- X-ray crystal structure of proliferating cell nuclear antigen 1 from Aeropyrum pernix.Acta crystallographica. Section F, Structural biology communications · 2024Article
36 more citing papers are in PubMed but not listed here.
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Authors and funding
49 authors.
Jasmine Y YoungRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA. Electronic address: jasmine.young@rcsb.org.
John D WestbrookRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Zukang FengRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Raul SalaRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Ezra PeisachRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Thomas J OldfieldProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Sanchayita SenProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Aleksandras GutmanasProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
David R ArmstrongProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
John M BerrisfordProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Li ChenRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Minyu ChenPDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
Luigi Di CostanzoRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Dimitris DimitropoulosRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Guanghua GaoRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Sutapa GhoshRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Swanand GoreProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Vladimir GuranovicRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Pieter M S HendrickxProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Brian P HudsonRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Reiko IgarashiPDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
Yasuyo IkegawaPDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
Naohiro KobayashiPDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
Catherine L LawsonRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Yuhe LiangRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Steve MadingBMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA.
Lora MakProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
M Saqib MirProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Abhik MukhopadhyayProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Ardan PatwardhanProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Irina PersikovaRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Luana RinaldiProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Eduardo Sanz-GarciaProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Monica R SekharanRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Chenghua ShaoRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
G Jawahar SwaminathanProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Lihua TanRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Eldon L UlrichBMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA.
Glen van GinkelProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Reiko YamashitaPDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
Huanwang YangRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Marina A ZhuravlevaRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Martha QuesadaRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Gerard J KleywegtProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Helen M BermanRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
John L MarkleyBMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA.
Haruki NakamuraPDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
Sameer VelankarProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Stephen K BurleyRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA.
Funding
Unified Data Resource for Large Complexes Determined by Cryo-Electron MicroscopyR01GM079429 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH · 2007 to 2021
$11.6MThe BMRB as an evolving resource for biomolecular structure-function researchR01GM109046 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI HOCH, JEFFREY C · 2014 to 2022
$6.6MBiotechnology and Biological Sciences Research Council BB/G022577/1Biotechnology and Biological Sciences Research Council BB/J007471/1Biotechnology and Biological Sciences Research Council BB/K016970/1Biotechnology and Biological Sciences Research Council BB/K020013/1Biotechnology and Biological Sciences Research Council BB/M011674/1Biotechnology and Biological Sciences Research Council BB/M013146/1Biotechnology and Biological Sciences Research Council BB/M020347/1Biotechnology and Biological Sciences Research Council BB/M020428/1Medical Research Council MR/L007835/1NIGMS NIH HHS R01 GM079429NIGMS NIH HHS R01 GM109046Wellcome Trust 104948Wellcome Trust 75968Wellcome Trust 88944
Abstract
OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments.
Indexed as
Databases, ProteinData CurationInternetModels, MolecularNuclear Magnetic Resonance, BiomolecularProtein ConformationProteinsUser-Computer InterfaceProteins3D macromolecular structurebiocurationdata archivingdata depositionPDBProtein Data Bankresearch datastructural biologyvalidationwwPDB
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