First contours of a vision for the future of validation at the PDB

From: Gerard DVD Kleywegt
Date: 14 October 2011 18:22


(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. Zwart.

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--Gerard