Newsletter | Winter 2016 ⋅ Number 68

Data Deposition and Annotation

In the fourth quarter of 2015, 2568 experimentally-determined structures were deposited to the PDB archive for a total of 10,955 entries deposited in the year. In 2014, 10,364 entries were deposited.

Of all structures deposited this year, 92.8% were determined by X-ray crystallographic methods; 4.6% were determined by NMR methods. 86% were deposited with a release status of hold until publication; 9% were released as soon as annotation of the entry was complete; and 5% were held until a particular date.

9388 new PDB structures were released in 2015. They account for 8% of the yearend total holdings of 114,697.

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.

Visit for more information on this new D&A system.

Videos demonstrate how to review and submit ligands with the wwPDB Deposition Tool.

For all ligands present in the uploaded coordinate file, the deposition system will search for graphical matches against all released ligands in the PDB. Close (but not exact) matches will require depositor attention as demonstrated here:


When the system cannot find a match for a ligand, depositors will be required to provide a SMILES or InChI string or a 2D chemical drawing, as shown in this video:

In 2015, the wwPDB hosted several events:

wwPDB/CCDC/D3R Ligand Validation Workshop (July 30-31, hosted by RCSB PDB at Rutgers): This meeting brought together co-crystal structure determination experts from academe and industry together with X-ray Crystallography and Computational Chemistry software developers to discuss and develop best practices for validation of co-crystal structures; editorial/refereeing standards for publishing co-crystal structures; and recommendations for ligand representation across the archive.

Advisory Committee Meeting (October 2, hosted by PDBj at Osaka University): The wwPDBAC is made up of an international team of experts in X-ray crystallography, cryoEM, NMR, and ioinformatics. The team, chaired by R. Andrew Byrd (National Cancer Institute at Frederick), meets annually to review presentations on wwPDB activities and plans for the future, and provide input on a range of topics and developments.

Symposium: Integrative Structural Biology with Hybrid Methods (October 2, hosted by PDBj at Osaka University): Several wwPDB AC members were joined by experts from Japan in sessions Integrative Structural Biology, the Power of Cryo-Electron Microscopy, Applications of Hybrid Methods, and Applications and Validations of Hybrid Methods. THE PROGRAM IS ONLINE This symposium was organized by the wwPDB Foundation and cosponsored by the Protein Research Foundation.

X-ray Validation Task Force (November 16-17, hosted by PDBe at EMBL-EBI): Method-specific Validation Task Forces have been convened to collect recommendations and develop consensus on additional validation that should be performed, and to identify software applications to perform validation tasks. Discussions at this year’s meeting of the X-ray Task Force included the recommendations from the Ligand Validation Workshop and a review of the current PDB validation report. 

PDBx/mmCIF Working Group (November 18, hosted by PDBe at EMBL-EBI): Chaired by Paul Adams (Lawrence Berkeley National Laboratory), the Working Group reviewed a variety of data representation topics.