OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Jasmine Y Young; John D Westbrook; Zukang Feng; Raul Sala; Ezra Peisach; Thomas J Oldfield; Sanchayita Sen; Aleksandras Gutmanas; David R Armstrong; John M Berrisford; Li Chen; Minyu Chen; Luigi Di Costanzo; Dimitris Dimitropoulos; Guanghua Gao; Sutapa Ghosh; Swanand Gore; Vladimir Guranovic; Pieter M S Hendrickx; Brian P Hudson; Reiko Igarashi; Yasuyo Ikegawa; Naohiro Kobayashi; Catherine L Lawson; Yuhe Liang; Steve Mading; Lora Mak; M Saqib Mir; Abhik Mukhopadhyay; Ardan Patwardhan; Irina Persikova; Luana Rinaldi; Eduardo Sanz-Garcia; Monica R Sekharan; Chenghua Shao; G Jawahar Swaminathan; Lihua Tan; Eldon L Ulrich; Glen van Ginkel; Reiko Yamashita; Huanwang Yang; Marina A Zhuravleva; Martha Quesada; Gerard J Kleywegt; Helen M Berman; John L Markley; Haruki Nakamura; Sameer Velankar; Stephen K Burley

doi:10.1016/j.str.2017.01.004

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Structure. 2017 Mar 7;25(3):536-545. doi: 10.1016/j.str.2017.01.004. Epub 2017 Feb 9.

Authors

Jasmine Y Young¹, John D Westbrook², Zukang Feng², Raul Sala², Ezra Peisach², Thomas J Oldfield³, Sanchayita Sen³, Aleksandras Gutmanas³, David R Armstrong³, John M Berrisford³, Li Chen², Minyu Chen⁴, Luigi Di Costanzo², Dimitris Dimitropoulos², Guanghua Gao², Sutapa Ghosh², Swanand Gore³, Vladimir Guranovic², Pieter M S Hendrickx³, Brian P Hudson², Reiko Igarashi⁴, Yasuyo Ikegawa⁴, Naohiro Kobayashi⁴, Catherine L Lawson², Yuhe Liang², Steve Mading⁵, Lora Mak³, M Saqib Mir³, Abhik Mukhopadhyay³, Ardan Patwardhan³, Irina Persikova², Luana Rinaldi³, Eduardo Sanz-Garcia³, Monica R Sekharan², Chenghua Shao², G Jawahar Swaminathan³, Lihua Tan², Eldon L Ulrich⁵, Glen van Ginkel³, Reiko Yamashita⁴, Huanwang Yang², Marina A Zhuravleva², Martha Quesada², Gerard J Kleywegt³, Helen M Berman², John L Markley⁵, Haruki Nakamura⁴, Sameer Velankar³, Stephen K Burley⁶

Affiliations

¹ 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.
² RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
³ Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
⁴ PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan.
⁵ BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA.
⁶ 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.

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.

Keywords: 3D macromolecular structure; PDB; Protein Data Bank; biocuration; data archiving; data deposition; research data; structural biology; validation; wwPDB.

Published by Elsevier Ltd.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural

MeSH terms

Data Curation
Databases, Protein
Internet
Models, Molecular
Nuclear Magnetic Resonance, Biomolecular
Protein Conformation
Proteins / chemistry*
User-Computer Interface

Substances

Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding