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[X-plor] First contours of a vision for the future of validation at the PDB

Gerard DVD Kleywegt via x-plor%40net.bio.net (by gerard from xray.bmc.uu.se)
Fri Oct 14 12:22:28 EST 2011

(Posted on behalf of wwPDB)

The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is pleased to direct PDB 
depositors and users to the recommendations of the wwPDB X-ray Validation Task 
Force (VTF) that were published in the journal Structure this week (2011, vol. 
19: 1395-1412; http://www.cell.com/structure/abstract/S0969-2126(11)00285-1).

The wwPDB X-ray VTF was convened in 2008 to collect expert recommendations and 
develop consensus on validation methods that should be applied to crystal 
structures (models and data) in the PDB and to identify software applications 
to perform these validation tasks. These recommendations are the basis of a 
new validation suite that will be part of the new Common Tool for Deposition 
and Annotation (D&A) that is currently being developed by the wwPDB partners. 
The D&A tool and the X-ray validation pipeline will go into production by the 
end of 2012 at all wwPDB deposition sites (RCSB PDB, PDBe, PDBj and BMRB). 
>From that moment in time on, depositors of X-ray crystal structures at the PDB 
will be provided with a detailed validation report. Such reports can be 
submitted to journals to accompany manuscripts describing new structures, and 
several publishers are working towards making such reports mandatory. Once the 
D&A tool is in production, the wwPDB partners also plan to provide the 
validation pipeline as a server, allowing crystallographers to assess their 
models before deposition and publication. Additional VTFs have been convened 
for NMR (by wwPDB) and 3DEM (by EMDataBank).

The wwPDB greatly appreciates the efforts of the authors of the X-ray VTF 
report: Randy J. Read, Paul D. Adams, W. Bryan Arendall III, Axel T. Brunger, 
Paul Emsley, Robbie P. Joosten, Gerard J. Kleywegt, Eugene B. Krissinel, 
Thomas Ltteke, Zbyszek Otwinowski, Anastassis Perrakis, Jane S. Richardson, 
William H. Sheffler, Janet L. Smith, Ian J. Tickle, Gert Vriend and Peter H. 



Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard from ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam  pdbe_admin from ebi.ac.uk

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