The Worldwide Protein Data Bank (wwPDB) partners are pleased to announce that X-ray structure validation reports can now be generated on demand by macromolecular crystallographers. Additional information including a link to the validation web server can be found at
The reports can be used to assess the quality of early, intermediate and near-final models to 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 been active since 2008 and has produced detailed recommendations to the wwPDB about how macromolecular crystal structures should be validated [1]. Many of these recommendations have already been implemented by wwPDB in a software pipeline [2] that has been in use since August 2013 to validate new depositions. “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.
Gerard Kleywegt was a member of the X-ray VTF until he moved to the ÀÖÌìÌÃÓÎÏ·ÍøÕ¾ in Cambridge in 2009, where he heads up the Protein Data Bank in Europe (PDBe), a wwPDB data center. One of the tasks in his new job is to oversee the implementation of the validation pipelines for X-ray, NMR and EM structural data and models. Kleywegt explains: “The X-ray VTF was eager for wwPDB to offer a publicly accessible stand-alone version of the validation pipeline. We think this will help crystallographers by enabling them to identify any problems with their models or data before they even write their papers or deposit. Ultimately, the goal is to improve the overall quality of structures described in the literature and deposited to the relevant archives, PDB, EMDB and BMRB.â€� Implementation of additional validation pipelines for structures based on NMR [3] and EM [4] data is in progress and these will be made publicly accessible in the future.
The stand-alone validation server was developed as part of a larger initiative - the new wwPDB Deposition and Annotation System. This new software system was developed to unify the data processing and annotation tools used across all wwPDB data centers. The new deposition system, currently in testing, will provide a single worldwide entry point for all experimental methods currently supported by the wwPDB. The new wwPDB annotation pipeline is a modular workflow driven system incorporating tools to manage validation as well as all of the chemical, sequence, structural and administrative annotation tasks. Helen Berman, director of the wwPDB data center at the RCSB PDB, says "By providing access to the tools used by the wwPDB to validate crystallographic data, the validation server will be an important tool for our depositors."
The X-ray validation pipeline produces reports that include results from tried and tested software, including MolProbity, Xtriage, Mogul, EDS and various CCP4 programs, as well as data processing and infrastructure applications developed by the wwPDB. The reports include the results of geometric checks, structure-factor assessment, and ligand validation. 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.
We welcome feedback on the new validation reports and the stand-alone server. If you would like to send us your comments or questions, then please contact [email protected]
