[3dem] Coming Soon: New NMR and 3DEM Validation Reports for Archived PDB Structures

[Ardan Patwardhan]

The wwPDB Partners and the EMDataBank are pleased to announce that validation reports for all Nuclear Magnetic Resonance (NMR) and 3D Cryo Electron Microscopy (3DEM) structures already represented in the global PDB archive will become publicly available in May.

The new validation reports will be 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)

The new validation reports assess the quality of each structure and highlight specific concerns, by examining the coordinates of the atomic model derived from either NMR and 3DEM, and by comparing the coordinates of the atomic model derived from NMR with primary experimental data therefrom. Readily interpretable summary information compares the quality of the atomic model with structural models from across the entire archive, thereby helping users of PDB data critically evaluate the quality of each archival entry.

The new validation reports implement recommendations provided by NMR and 3DEM community experts on validation, while reusing elements of the validation schema developed for structures determined by X-ray crystallography. The X-ray, NMR, and 3D EM method specific validation pipelines were developed in the context of a larger global wwPDB initiative, the new common wwPDB Deposition and Annotation System, which was created to unify deposition, annotation, and validation practices used across all wwPDB partner sites.

Since January 2016, the new NMR and 3DEM structure-validation reports have been provided to depositors as part of the wwPDB Deposition and Annotation System to help identify potential problems that should be addressed prior to PDB deposition and publication.

Further information, including the new Validation Report User Guide, is available. We welcome your feedback. Please send any comments or questions to validation at mail.wwpdb.org.




Ardan Patwardhan
Coordinator - cellular structure & PDBe production
Protein Data Bank in Europe (PDBe)
European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Tel: +44 1223 492649

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