All validation reports for released PDB and EMDB entries have been
updated and are now available with recalculated percentiles. In
addition, validation reports now include new percentile statistics
reflecting the state of the PDB archive on December 31, 2025, EDS
https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_protein_na_chains
and MolProbity updates, new Q-score percentile
https://www.wwpdb.org/news/news?year=2025#68c9b3a1829c3fea8eaf394d
information, and ligand validation improvements.
Ligand validation improvements were made in response to feedback from
Global Phasing Ltd., reporting that wwPDB validation software queries of
the CSD via Mogul returned insufficient results for such common moieties
as adenine, leading to an incorrect rendering of geometric quality in
the buster-report-like diagrams. This was traced to a mismatch in
aromaticity specifications between wwPDB validation software and Mogul,
that has now been updated. In addition, a depiction of non-carbon atoms
by grey balls has been added to these diagrams.
The updated reports are accessible from:
A snapshot of the previous version on 20260415 is archived at RCSB PDB
https://pdbsnapshots.s3.us-west-2.amazonaws.com/index.html#20260415/
and PDBj https://snapshots.pdbj.org/20260415/.
These updated wwPDB validation reports provide an assessment of
structure quality using widely accepted standards and criteria,
recommended by community experts serving on Validation Task Forces
https://www.wwpdb.org/task/validation-task-forces.
Validation reports are provided to depositors through OneDep--the wwPDB
portal for validation, deposition and biocuration of structure data.
wwPDB partners encourage the use of the stand-alone validation server
http://validate.wwpdb.org/ and the web service 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, NMR, EM, and as we collect feedback from depositors and users
https://www.wwpdb.org/task/validation-task-forces.
The wwPDB partners strongly encourage journal editors and referees to
request reports from authors as part of the manuscript submission and
review process, as 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. Reports are date-stamped, display the wwPDB logo, and represent
standardized wwPDB validation.
Further information and sample validation reports are available
https://www.wwpdb.org/validation/validation-reports.
Your feedback, comments, and questions are welcome at
validation@mail.wwpdb.org.
Please read the full news here:
https://www.wwpdb.org/news/news?year=2026#69e128796c4fcd38cafe946d
On behalf of the wwPDB
--
IRINA PERSIKOVA, Ph.D.
Deputy Biocuration Lead, RCSB Protein Data Bank
Research Associate, Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
P: 848.445.4938 | E: irina.persikova@rcsb.org
rcsb.org <www.rcsb.org> | iqb.rutgers.edu http://iqb.rutgers.edu |
facebook https://www.facebook.com/RCSBPDB | twitter
https://twitter.com/buildmodels
All validation reports for released PDB and EMDB entries have been
updated and are now available with recalculated percentiles. In
addition, validation reports now include new percentile statistics
reflecting the state of the PDB archive on December 31, 2025, EDS
<https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_protein_na_chains>
and MolProbity updates, new Q-score percentile
<https://www.wwpdb.org/news/news?year=2025#68c9b3a1829c3fea8eaf394d>
information, and ligand validation improvements.
Ligand validation improvements were made in response to feedback from
Global Phasing Ltd., reporting that wwPDB validation software queries of
the CSD via Mogul returned insufficient results for such common moieties
as adenine, leading to an incorrect rendering of geometric quality in
the buster-report-like diagrams. This was traced to a mismatch in
aromaticity specifications between wwPDB validation software and Mogul,
that has now been updated. In addition, a depiction of non-carbon atoms
by grey balls has been added to these diagrams.
The updated reports are accessible from:
* https://files.wwpdb.org/pub/pdb/validation_reports/ (wwPDB)
* https://files.rcsb.org/pub/pdb/validation_reports/ (RCSB PDB)
* ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ (PDBe)
* https://files.pdbj.org/pub/pdb/validation_reports/ (PDBj)
A snapshot of the previous version on 20260415 is archived at RCSB PDB
<https://pdbsnapshots.s3.us-west-2.amazonaws.com/index.html#20260415/>
and PDBj <https://snapshots.pdbj.org/20260415/>.
These updated wwPDB validation reports provide an assessment of
structure quality using widely accepted standards and criteria,
recommended by community experts serving on Validation Task Forces
<https://www.wwpdb.org/task/validation-task-forces>.
Validation reports are provided to depositors through OneDep--the wwPDB
portal for validation, deposition and biocuration of structure data.
wwPDB partners encourage the use of the stand-alone validation server
<http://validate.wwpdb.org/> and the web service 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, NMR, EM, and as we collect feedback from depositors and users
<https://www.wwpdb.org/task/validation-task-forces>.
The wwPDB partners strongly encourage journal editors and referees to
request reports from authors as part of the manuscript submission and
review process, as 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. Reports are date-stamped, display the wwPDB logo, and represent
standardized wwPDB validation.
Further information and sample validation reports are available
<https://www.wwpdb.org/validation/validation-reports>.
Your feedback, comments, and questions are welcome at
validation@mail.wwpdb.org.
Please read the full news here:
https://www.wwpdb.org/news/news?year=2026#69e128796c4fcd38cafe946d
On behalf of the wwPDB
--
IRINA PERSIKOVA, Ph.D.
Deputy Biocuration Lead, RCSB Protein Data Bank
Research Associate, Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
P: 848.445.4938 | E: irina.persikova@rcsb.org
rcsb.org <www.rcsb.org> | iqb.rutgers.edu <http://iqb.rutgers.edu> |
facebook <https://www.facebook.com/RCSBPDB> | twitter
<https://twitter.com/buildmodels>