Bringing Structure to Biology
Overview of PDB Validation Reports published in Structure
An article focused on the structure validation reports produced by wwPDB is now available: Validation of Structures in the Protein Data Bank (2017) Structure doi: 10.1016/j.str.2017.10.009.
The paper describes how validation reports for PDB structures determined by X-ray crystallography were first made available to depositors in 2013 and added to the PDB archive in 2014. In early 2016, following the update of the OneDep system, reports for structures solved by nuclear magnetic resonance and 3D electron microscopy were made available to the depositors and later incorporated into the PDB archive.
These reports are based on the published recommendations of expert Validation Task Forces appointed by the wwPDB and EMDataBank partners. Preliminary reports are generated at a stand-alone webserver (validate.wwpdb.org), during deposition in OneDep (deposit.wwpdb.org) or programmatically via a web service API. The wwPDB partners strongly recommend the use of these options to verify structure quality prior to data submission to the PDB archive. Following biocuration, an official wwPDB structure validation report is produced, which should be submitted to journals along with manuscripts describing the structure. Upon public release of a PDB entry, the corresponding validation report is also made public in the PDB archive.