Dear all,
We are pleased to announce the publication of this manuscript,
addressing the challenge of validation of experimental biomolecular NMR
structures against restraint data.
The NMR exchange (NEF) and NMR-STAR formats provide a standardized
approach for representing commonly used NMR restraints. Using these
restraint formats, a standardized validation system for assessing
structural models of biopolymers against restraints has been developed
and implemented in the wwPDB OneDep data harvesting system.
The resulting wwPDB Restraint Violation Report provides a model vs data
assessment of biomolecule structures determined using distance and
dihedral restraints, with extensions to other restraint types currently
being implemented. These tools are useful for assessing NMR models, as
well as for assessing biomolecular structure predictions based on
distance restraints.
We present the rationale for model-vs-data restraint validation by the
wwPDB, together with summary of validation tools and reports for NMR
distance and dihedral restraints that have been developed, as
implemented in the wwPDB validation pipeline and recommended by the
wwPDB NMR-VTF committee.
*Restraint Validation of Biomolecular Structures Determined by NMR
in the Protein Data Bank*
Kumaran Baskaran, Eliza Ploskon, Roberto Tejero, Masashi Yokochi,
Deborah Harrus, Yuhe Liang, Ezra Peisach, Irina Persikova, Theresa A
Ramelot, Monica Sekharan, James Tolchard, John D Westbrook, Benjamin
Bardiaux, Charles Schwieters, Ardan Patwardhan, Sameer Velankar,
Stephen K Burley, Genji Kurisu, Jeffrey C Hoch, Gaetano T
Montelione, Geerten W Vuister, Jasmine Y Young
(2024)/Structure/32, 1–14: doi:10.1016/j.str.2024.02.011
<https://doi.org/10.1016/j.str.2024.02.011>
The wwPDB plans to further enhance validation report by providing
model-vs-data quality assessment for other kinds of restraints based on
community recommendation and improve data representation on structures
with multiple conformation states.
Kind regards,
Deborah Harrus, on behalf of the wwPDB
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Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - 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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