22-May-2013

Deposition and Release of PDB Entries Containing Large Structures

In order to meet the challenges of ever greater numbers of PDB depositions, involving ever larger and more complex structures, often determined using multiple methods, the Worldwide Protein Data Bank partners (wwPDB; http://wwpdb.org/) are developing a completely new system for deposition and annotation of PDB entries. This new system will go into full production at all the wwPDB deposition sites early in 2014 and will then be able to handle depositions of structures of any size, determined using diffraction, NMR and/or EM methods. Large structures will also be processed and released intact so that "split entries" become a thing of the past.

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2-April-2013

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

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/. It is updated as new entries are added to the PDB archive. An overview of BIRD, along with definition details, is available online.

These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users worldwide.