[bmrblist] Updated Validation Reports for Archived PDB Structures Now Available

Kumaran Baskaran kbaskaran at bmrb.wisc.edu
Tue Mar 21 10:25:00 CDT 2017


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
<ftp://snapshots.wwpdb.org/20170308/pub/> and PDBj
<ftp://snapshots.pdbj.org/20170308/pub/>.

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
<https://www.wwpdb.org/task/validation-task-forces>. 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<http://validate.wwpdb.org/> and the webservice API
<https://www.wwpdb.org/validation/onedep-validation-web-service-interface> 
  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<https://www.wwpdb.org/task/xray>, NMR
<https://www.wwpdb.org/task/nmr>, EM<https://www.wwpdb.org/task/em>,
and on ligand validation, and as we collect feedback from depositors and
users.

Further information and sample validation reports are available
<https://www.wwpdb.org/validation/validation-reports>.

Your feedback, comments, and questions are welcome at
validation at mail.wwpdb.org <mailto:validation at mail.wwpdb.org>.


Best regards,

Kumaran Baskaran

BMRB

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