The Worldwide Protein Data Bank (wwPDB) partners are pleased to announce
that validation reports for all X-ray crystal structures in the PDB
archive are now publicly available.
The new validation reports are set to become an indispensable resource
for both crystallographers and the consumers of structural data who
increasingly need to critically assess and compare PDB entries.
The reports implement the recommendations of a large group of community
experts on validation and include the results of geometric checks,
structure-factor assessment and ligand validation. The reports include
results from tried and tested software including MolProbity, Xtriage,
Mogul, EDS and various CCP4 programs. They summarise the quality of the
structure and highlight specific concerns by considering the coordinates
of the model, the diffraction data and the fit between the two. Easily
interpretable summary information that compares the quality of a
structure with that of other structures in the archive is also provided.
Validation reports for all X-ray structures archived in the PDB are
accessible from the following FTP sites:
* ftp://ftp.wwpdb.org/pub/pdb/validation_reports/ (wwPDB)
* ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ (PDBe)
* ftp://ftp.pdbj.org/pub/pdb/validation_reports/ (PDBj)
The new X-ray structure validation reports have been provided to
depositors as part of the structure-annotation process since August
2013. More recently, a stand-alone wwPDB X-ray structure validation
server was launched (http://wwpdb-validation.wwpdb.org/). The server
allows crystallographers to check early, intermediate and near-final
models on demand and helps identify any potential problems that need
addressing prior to structure analysis, publication and deposition.
"The stand-alone validation server will run exactly the same validation
tests that have recently been introduced for the annotation of new
depositions," says Randy Read of Cambridge University. Read chairs the
wwPDB X-ray Validation Task Force (VTF) that has produced detailed
recommendations to the wwPDB about how macromolecular crystal structures
should be validated [1]. "With the stand-alone server, crystallographers
won't have any last-minute surprises when they deposit their structures
just before submitting the paper," Read adds.
The reports have been developed in the context of a larger initiative,
the new wwPDB Deposition and Annotation system
(http://wwpdb.org/system_info.html), which was created to unify the
annotation tools and practices used across all wwPDB deposition centres
and for all common structure-determination methods.
About wwPDB
wwPDB (http://wwpdb.org) is the international partnership that manages
the PDB archive. It consists of: the Research Collaboratory for
Structural Bioinformatics Protein Data Bank (RCSB PDB; http://rcsb.org)
and BioMagResBank (BMRB; http://bmrb.wisc.edu) in the USA, the Protein
Data Bank in Europe (PDBe; http://pdbe.org) and the Protein Data Bank
Japan (PDBj; http://pdbj.org). Together, the wwPDB partners are
committed to ensuring high standards of quality, integrity and
consistency of this uniquely important archive and to make it freely
available for the benefit of scientists worldwide.
[1] Read R. J., Adams P. D., Arendall III W. D., Brünger A. T., Emsley
P., Joosten R. P., Kleywegt G. J., Krissinel E. B., Lütteke T.,
Otwinowski Z., Perrakis A., Richardson J. S., Sheffler W. H., Smith J.
L., Tickle I. J., Vriend G., and Zwart P. H. A new generation of
crystallographic validation tools for the Protein Data Bank. Structure,
19, 1395-1412, 2011. DOI: 10.1016/j.str.2011.08.006
--
Gary Battle
Protein Data Bank in Europe (PDBe)
EMBL-EBI
http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope
