Newsletter | Spring 2016 ⋅ Number 69
In the first quarter of 2016, 2883 experimentally-determined structure coordinate entries were deposited to the archive.
84.0% were deposited with a release status of hold until publication; 9.3% were released as soon as annotation of the entry was complete; and 6.7% were held until a particular date.
89.9% of these entries were determined by X-ray crystallographic methods; 4.5% were determined by NMR methods.
During the same period, 2776 structures and 245 EMDB maps were released in the PDB.
Since January 2014, the new wwPDB Deposition & Annotation (D&A) system has been used to submit and annotate >12,000 X-ray structure depositions and to release >6,800 entries in the PDB archive.
The wwPDB has now expanded this system to support structures from 3DEM and NMR experiments. The wwPDB D&A system interoperates with EMDB and BMRB to enable joint depositions of both atomic coordinates (PDB) and electron density maps (EMDB) or NMR experimental data (BMRB). Both PDB and EMDB/BMRB accession codes will be issued simultaneously after the entry is deposited.
Starting May 31st 2016, legacy deposition systems AutoDep, ADIT-NMR (BMRB|PDBj), and EMDep will no longer accept new PDB and EMDB submissions. Depositors with in-progress sessions on the legacy systems will be able to access and complete their deposition sessions until September 30th 2016.
An updated ADIT-NMR system (available from BMRB and PDBj-BMRB) will continue to accept NMR data associated with a structure currently not accepted by the unified wwPDB deposition system (for example, relaxation data, and primary time-domain spectra) as well as experimental NMR data not associated with the deposition of 3D coordinates.
Visit wwpdb.org for more information.
Effective May 8th 2016, depositors submitting PDB data will have the option to suppress the entry's author list and title prior to public release of the structure. This functionality will be available on an opt in basis. Depositors who opt in will have their entry author list and title hidden from searches of unreleased PDB structures.
This option is being added to the wwPDB Deposition, Annotation, and Validation System at the request of the depositor community.
It is anticipated that this feature will benefit the manuscript review process. Journals will be able to request wwPDB validation reports to enable more informed referee review, while respecting depositor confidentiality. Depositors are strongly encouraged to complete their data submissions before manuscript submission to the journals. Depositors are similarly encouraged to provide the official wwPDB validation report to the journals at the time of manuscript submission.
wwPDB Validation Reports provide an assessment of structure quality using widely accepted standards and criteria, as recommended by community experts serving in the Validation Task Force. They are provided to depositors during annotation, with review required in the Deposition & Annotation system.
The wwPDB partners strongly encourage journal editors and referees to request these reports from authors as part of the manuscript submission and review process. Provision is already required by eLife, The Journal of Biological Chemistry, the International Union of Crystallography (IUCr) journals, FEBS Journal, and the Journal of Immunology.
Going forward, validation reports will be further improved as wwPDB receives recommendations from the expert Validation Task Forces (VTF) for X-ray, NMR, and EM; develops the wwPDB Deposition & Annotation system; and collects feedback from depositors and users.
In March, wwPDB released updated validation reports for all X-ray crystal structures deposited in the PDB archive. These reports are available from the wwPDB partner sites as well as from RCSB PDB Structure Summary pages.
These updated reports now include:
A snapshot of the reports previously available has been archived at RCSB PDB and PDBj.
Similar reports for structures determined by Nuclear Magnetic Resonance (NMR) and 3D Cryo Electron Microscopy (3DEM) will become available in May 2016.
For more information, visit wwpdb.org.
