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Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank
Spring 2013
Number 57

NEWSLETTER

Data Deposition and Annotation

Deposition Statistics

´╗┐In the first quarter of 2013, 2501 experimentally-determined structure coordinates and 127 3DEM maps were deposited to the archive.

84% were deposited with a release status of hold until publication; 13.5% were released as soon as annotation of the entry was complete; and 2.6% were held until a particular date. 92.6% of these entries were determined by X-ray crystallographic methods; 5.7% were determined by NMR methods.

During the same period, 2166 structures were released in the PDB.


Revision History Widget


´╗┐ The Revision History box shows the modification date and a summary description; mousing over the text provides additional details.

Structure Summary pages offer a variety of information about an entry, organized into different widget boxes that can be moved around on the page.

The Revision History widget box displays the details of changes made to an entry's mmCIF/PDBx file after the initial release. The details of these changes have been recorded in the category PDBX_VERSION since July 2011 (see the wwpdb.org for more information).

These descriptions are more detailed than the information stored in REVDAT records, which indicate what records have been changed in the PDB format file for the entry.


wwPDB News

The Biologically Interesting Molecule Reference Dictionary (BIRD) for Peptide-like Antibiotic and Inhibitor Molecules


´╗┐Chloroorienticin A has a disaccharide and a monosaccharide decorating the peptide core (PRD_000203)

The wwPDB's Biologically Interesting molecule Reference Dictionary (BIRD) describes antibiotics, peptide inhibitors, and other complex biological ligands. To help define and represent these biologically interesting molecules, BIRD contains chemical descriptions, sequence and linkage information, and functional and classification information as taken from the core structures and from external resources.

All PDB entries containing these molecules have been annotated using this dictionary, with corresponding BIRD ID code contained only in the PDBx-formatted file. The use of BIRD will greatly improve the consistency of peptide-like antibiotic and inhibitor molecules in the PDB.

BIRD is available on the wwPDB FTP server adjacent to the Chemical Component Dictionary at ftp://ftp.wwpdb.org/pub/pdb/data/bird/prd/.