Dear all,
A new publication describes two percentile-based metrics:
/Q/_relative_all and /Q/_relative_resolution. The publication presents a
statistical analysis of Q-score and these new percentile based
validation metrics (expanded on below).
/*Q*/*_relative_all* is a single value percentile, representing the
overall quality of the model-map fitness. It is derived by comparing a
model-map average /Q/-score to all model-map average Q-scores calculated
for 3DEM structures in the PDB/EMDB. Higher /Q/_relative_all percentile
values, infer higher quality in the model-map fitness.
/*Q*/*_relative_resolution* is a single value percentile, derived by
comparing the average /Q/-score of a model-map with the /Q/-scores of
other model-map entries of similar resolution. This metric was developed
from the principle that average Q-score is correlated with map
resolution. /Q/_relative_resolution percentile values close to 50%
therefore represent a score that is commonly observed for entries in the
PDB/EMDB of similar resolution, inferring model-map fitness is typical
for an entry of a particular resolution. Notably low or high
/Q/_relative_resolution percentiles may be helpful to guide further
review of model-maps.
The EMDB has made these metrics available since Spring 2024 via
emdatabank.org <http://emdatabank.org/> and since the publication of the
paper, the wwPDB is in the process of incorporating these metrics into
wwPDB validation reports by providing the Q-score percentile slider for
the assessment of model-map fitness of 3DEM entries. This validation
enhancement will help depositors, reviewers and the community to improve
the quality of data submissions and assist users to assess 3DEM data
quality in the PDB and EMDB, wwPDB core archives.
q-score_wwPDB_news.png
*Q-score as a reliability measure for protein, nucleic acid and
small-molecule atomic coordinate models derived from 3DEM maps*
Grigore Pintilie, Chenghua Shao, Zhe Wang, Brian P Hudson, Justin W
Flatt, Michael F Schmid, Kyle L Morris, Stephen K Burley, Wah Chiu.
(2025) /Acta Cryst/ D81: 410-422 doi: 10.1107/S2059798325005923
<https://doi.org/10.1107/s2059798325005923>
Please find the full news here:
https://www.wwpdb.org/news/news?year=2025#689f2e8a3b59581b680197a2
Best wishes,
Deborah Harrus, on behalf of the wwPDB
--
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Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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