Data Deposition and Annotation

In the second quarter of 2015, 2518 experimentally-determined structure coordinate entries were deposited to the archive. A total of 5407 entries have been deposited in the first half of this year.

85.6% were deposited with a release status of hold until publication; 9.5% were released as soon as annotation of the entry was complete; and 4.9% were held until a particular date.

92.7% of these entries were determined by X-ray crystallographic methods; 5.3% were determined by NMR methods.

During the same period, 2236 structures and 115 EMDB maps were released in the PDB.

As announced previously, the weekly public release of data from the Protein Data Bank (PDB) archive is now divided into two phases to serve better the needs of methods developers focused on protein structure prediction and protein-ligand docking. Going forward on a weekly basis, these developer communities will have ~4 days during which they can make blind predictions of protein or nucleic acid structure from polymer sequence and ligand docking pose from polymer sequence and the InChI string of bound ligand.

• Phase I: Every Saturday by 3:00 UTC, for every new entry, the wwPDB website provides: sequence(s) (amino acid or nucleotide) for each distinct polymer (new_release_structure_sequence.tsv) and, where appropriate, the InChI string(s) for each distinct ligand (new_release_structure_nonpolymer.tsv)
• Phase II: Every Wednesday by 00:00 UTC, all new and modified data entries will be updated at each of the wwPDB FTP sites.

As announced in January, ADIT will be retired on July 19, 2015 for structures determined using X-ray crystallography. Any in-progress ADIT X-ray deposition sessions need to be completed before that time.

wwPDB launched the Deposition Tool for structures determined using X-ray crystallography on January 27, 2014 as part of a new Deposition and Annotation System. Using this system, more than 7,600 structures have been deposited and annotated, and more than 3,500 structures released in the archive.

Features of the new system include use of the PDBx/mmCIF data format, which produces more uniform data; the ability to replace data files pre- and post-deposition; enhanced communication; improved annotation; and geometric and experimental data checking based on recommendations from expert task forces. Detailed information and video tutorials are available.

ADIT will continue to accept depositions from other experimental methods. Deposition tools for NMR and 3DEM are being developed by the wwPDB.

Questions and comments should be sent to info@wwpdb.org.

RCSB PDB Biocuration Team Lead Jasmine Young visited wwPDB collaborator PDBj on her way to the Biocuration meeting.