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Updated Validation Reports for Archived PDB Structures Now Available

03/15

The wwPDB partners are pleased to announce that updated validation reports for all X-ray, NMR, and 3DEM structures deposited in the PDB archive are now available on March 15, 2017.

The updates include new percentile statistics reflecting the state of the PDB archive on December 31th 2016 and updated versions of the Mogul software (2017) and CSD archive (as538be).

The updated reports are accessible from the following FTP sites:

  • ftp://ftp.wwpdb.org/pub/pdb/validation_reports/ (wwPDB)
  • ftp://ftp.rcsb.org/pub/pdb/validation_reports/ (RCSB PDB)
  • ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ (PDBe)
  • ftp://ftp.pdbj.org/pub/pdb/validation_reports/ (PDBj)

A copy of the previous version is archived at RCSB PDB and PDBj.

These updated wwPDB validation reports provide an assessment of structure quality using widely accepted standards and criteria, recommended by community experts serving in the Validation Task Force. The wwPDB partners strongly encourage journal editors and referees to request them from authors as part of the manuscript submission and review process. The reports are date-stamped and display the wwPDB logo, and contain the same information, regardless of which wwPDB site processed the entry. Provision of wwPDB validation reports is already required by Nature, eLife, The Journal of Biological Chemistry, the International Union of Crystallography (IUCr) journals, FEBS journals, Journal of Immunology and Angew Chem Int Ed Engl as part of their manuscript-submission process.

Validation reports are also provided to depositors through OneDep - the wwPDB portal for validation, deposition and biocuration of structure data. The wwPDB partners encourage the use of the stand-alone validation server and the webservice API at any time prior to data deposition. Depositors are required to review and accept the reports as part of the data submission process. Validation reports will continue to be developed and improved as we receive recommendations from the expert Validation Task Forces (VTF) for X-ray, NMR, EM, and on ligand validation, and as we collect feedback from depositors and users.

Further information and sample validation reports are available.

Your feedback, comments, and questions are welcome at validation@mail.wwpdb.org.