title: OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.
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.
authors.affiliation: RCSB 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.
authors.forename: Jasmine Y
authors.initials: JY
authors.lastname: Young
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: John D
authors.initials: JD
authors.lastname: Westbrook
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Zukang
authors.initials: Z
authors.lastname: Feng
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Raul
authors.initials: R
authors.lastname: Sala
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Ezra
authors.initials: E
authors.lastname: Peisach
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Oldfield
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Sanchayita
authors.initials: S
authors.lastname: Sen
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Aleksandras
authors.initials: A
authors.lastname: Gutmanas
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: David R
authors.initials: DR
authors.lastname: Armstrong
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: John M
authors.initials: JM
authors.lastname: Berrisford
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.affiliation: PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
authors.forename: Minyu
authors.initials: M
authors.lastname: Chen
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Luigi
authors.initials: L
authors.lastname: Di Costanzo
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Dimitris
authors.initials: D
authors.lastname: Dimitropoulos
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Guanghua
authors.initials: G
authors.lastname: Gao
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Sutapa
authors.initials: S
authors.lastname: Ghosh
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Swanand
authors.initials: S
authors.lastname: Gore
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Guranovic
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Pieter M S
authors.initials: PMS
authors.lastname: Hendrickx
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Hudson
authors.affiliation: PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
authors.forename: Reiko
authors.initials: R
authors.lastname: Igarashi
authors.affiliation: PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
authors.forename: Yasuyo
authors.initials: Y
authors.lastname: Ikegawa
authors.affiliation: PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
authors.forename: Naohiro
authors.initials: N
authors.lastname: Kobayashi
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Catherine L
authors.initials: CL
authors.lastname: Lawson
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Yuhe
authors.initials: Y
authors.lastname: Liang
authors.affiliation: BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Steve
authors.initials: S
authors.lastname: Mading
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Lora
authors.initials: L
authors.lastname: Mak
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: M Saqib
authors.initials: MS
authors.lastname: Mir
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Abhik
authors.initials: A
authors.lastname: Mukhopadhyay
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Ardan
authors.initials: A
authors.lastname: Patwardhan
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Irina
authors.initials: I
authors.lastname: Persikova
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Luana
authors.initials: L
authors.lastname: Rinaldi
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Sanz-Garcia
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Monica R
authors.initials: MR
authors.lastname: Sekharan
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Chenghua
authors.initials: C
authors.lastname: Shao
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: G Jawahar
authors.initials: GJ
authors.lastname: Swaminathan
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Lihua
authors.initials: L
authors.lastname: Tan
authors.affiliation: BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Eldon L
authors.initials: EL
authors.lastname: Ulrich
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Glen
authors.initials: G
authors.lastname: van Ginkel
authors.affiliation: PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
authors.forename: Reiko
authors.initials: R
authors.lastname: Yamashita
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Huanwang
authors.initials: H
authors.lastname: Yang
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Marina A
authors.initials: MA
authors.lastname: Zhuravleva
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Martha
authors.initials: M
authors.lastname: Quesada
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Gerard J
authors.initials: GJ
authors.lastname: Kleywegt
authors.affiliation: RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Helen M
authors.initials: HM
authors.lastname: Berman
authors.affiliation: BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: John L
authors.initials: JL
authors.lastname: Markley
authors.affiliation: PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
authors.forename: Haruki
authors.initials: H
authors.lastname: Nakamura
authors.affiliation: Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Sameer
authors.initials: S
authors.lastname: Velankar
authors.affiliation: RCSB 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.
authors.forename: Stephen K
authors.initials: SK
authors.lastname: Burley
mesh_terms: D066289:Data Curation; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D014584:User-Computer Interface
chemical_list: D011506:Proteins
keywords: 3D macromolecular structure; PDB; Protein Data Bank; biocuration; data archiving; data deposition; research data; structural biology; validation; wwPDB