The wwPDB is continuing to improve and expand our validation offerings
with a new addition to the wwPDB PDF validation reports. Building on the
success of the coordinate‑model percentile sliders, which help
depositors, reviewers, and archive users assess PDB model quality in the
context of the PDB archive, we are now extending this section to include
a Q-score
https://journals.iucr.org/d/issues/2025/08/00/ic5125/index.html
percentile slider. The new slider is the first to empower users of this
report to assess model-map quality at a glance relative to the EMDB/PDB
archives.
Starting October 01, newly released 3DEM entries will include the
Q‑score percentile slider
https://www.wwpdb.org/validation/2017/EMValidationReportHelp in its
own section below the current sliders under “Overall quality at a
glance.” The slider compares an entry’s average Q‑score against both the
entire EMDB/PDB archive and a resolution‑similar subset. Because Q‑score
correlates strongly with resolution between 1–10 Å, the percentile helps
check whether a reported global resolution is reasonable; unusually low
values can flag model–map fit or map quality issues. A dedicated Q‑score
section supports deeper review with residue‑level mapping to the
coordinate model and per‑chain tables.
In the near future, wwPDB will re-generate validation reports with
Q-score slider for all existing entries in the PDB archive.
We are excited for our users to get their hands on this new validation
metric. If you have any queries or feedback please let us know at
info@wwpdb.org.
Please read the full news here:
https://www.wwpdb.org/news/news?year=2025#68c9b3a1829c3fea8eaf394d
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
mailto:irina.persikova@rcsb.org
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