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Comment on Timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013).
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MedLine Citation:
PMID:  24311570     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
The wwPDB responds to the article by Joosten et al. [(2013), Acta Cryst. D69, 2293-2295].
Authors:
Helen Berman; Gerard J Kleywegt; Haruki Nakamura; John L Markley
Publication Detail:
Type:  Journal Article     Date:  2013-11-19
Journal Detail:
Title:  Acta crystallographica. Section D, Biological crystallography     Volume:  69     ISSN:  1399-0047     ISO Abbreviation:  Acta Crystallogr. D Biol. Crystallogr.     Publication Date:  2013 Dec 
Date Detail:
Created Date:  2013-12-06     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9305878     Medline TA:  Acta Crystallogr D Biol Crystallogr     Country:  United States    
Other Details:
Languages:  eng     Pagination:  2296     Citation Subset:  IM    
Affiliation:
Department of Chemistry & Chemical Biology, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA.
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Journal Information
Journal ID (nlm-ta): Acta Crystallogr D Biol Crystallogr
Journal ID (iso-abbrev): Acta Crystallogr. D Biol. Crystallogr
Journal ID (publisher-id): Acta Cryst. D
ISSN: 0907-4449
ISSN: 1399-0047
Publisher: International Union of Crystallography
Article Information
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A full version of this article is available from Crystallography Journals Online.© Berman et al. 2013
open-access:
Received Day: 18 Month: 10 Year: 2013
Accepted Day: 22 Month: 10 Year: 2013
Print publication date: Day: 01 Month: 12 Year: 2013
Electronic publication date: Day: 19 Month: 11 Year: 2013
pmc-release publication date: Day: 19 Month: 11 Year: 2013
Volume: 69 Issue: Pt 12
First Page: 2296 Last Page: 2296
PubMed Id: 24311570
ID: 3852647
Publisher Id: be5245
DOI: 10.1107/S0907444913029168
Coden: ABCRE6
Publisher Item Identifier: S0907444913029168

Comment on Timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013) Alternate Title:Comment
Helen Bermana*
Gerard J. Kleywegtb
Haruki Nakamurac
John L. Markleyd
aDepartment of Chemistry & Chemical Biology, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
bPDBe, European Molecular Biology Laboratory–European Bioinformatics Institute, Cambridge CB10 1SD, UK
cPDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
dBioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
Correspondence: Correspondence e-mail: berman@rcsb.rutgers.edu

The Worldwide Protein Data Bank (wwPDB) strongly agrees with the overall views expressed by Joosten et al. (2013) in their article about timely deposition of macromolecular structures in the Protein Data Bank. In 2010, Acta Crystallographica Section D began to require validation reports as part of the manuscript-submission process. In that same year, the wwPDB sent letters to the key journals that publish structures requesting that they require authors to submit wwPDB validation reports at the same time as their manuscripts. In this way, reviewers are able to better evaluate the work. The Journal of Biological Chemistry, which is currently the journal that publishes the largest number of papers per year about structures of biological macromolecules, began requiring these reports in 2012.

Joosten et al. suggest that it would be helpful to have an option to suppress entry titles at the time of submission to the PDB until the structure is released. Policy matters such as this are regularly reviewed by the wwPDB partners and its Advisory Committee (wwPDB AC). The issue was discussed at our 2013 meeting, and it was agreed that we will make this option available in the new wwPDB Deposition Tool that will be launched early in 2014.


References
Joosten, R. P., Soueidan, H., Wessels, L. F. A. & Perrakis, A. (2013). Acta Cryst. D69, 2293–2295.

Article Categories:
  • Letters to the Editor

Keywords: wwPDB, deposition, macromolecular data.

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