wwPDB 2006 News

Contents

12/29/2006 ADVISORY COMMITTEE MEETING
11/28/2006 wwPDB Paper Published
08/15/2006 Phasing Out Theoretical Model Depositions to the PDB Archive
06/21/2006 wwPDB Statistics Available
04/27/2006 ADVISORY COMMITTEE MEETING

12/29/2006

ADVISORY COMMITTEE MEETING

The third meeting of the world wide Protein Data Bank Advisory Committee (wwPDBAC) was held in Tokyo, Japan on October 27, 2006. The report of the meeting is available in PDF format.

11/28/2006

wwPDB Paper Published

A paper describing the wwPDB - data deposition and access information, data uniformity efforts, and more - has been published:

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
Helen Berman; Kim Henrick; Haruki Nakamura; John L. Markley
Nucleic Acids Research 2006; doi: 10.1093/nar/gkl971

08/15/2006

Phasing Out Theoretical Model Depositions to the PDB Archive

Effective October 15, 2006, PDB depositions will be restricted to atomic coordinates that are substantially determined by experimental measurements on specimens containing biological macromolecules. This policy was recommended and endorsed by a working group comprised of structural and computational biologists and endorsed by the wwPDB advisory committee. Thus, theoretical model depositions (such as models determined purely in silico using, for example, homology or ab initio methods) will no longer be accepted.

Theoretical models that have been previously released or that will be released from now until October 15, 2006 will continue to be publicly available via the existing models archive at ftp://ftp.rcsb.org/pub/pdb/data/structures/models/current/.

A summary of the implementation plan for the phasing out of theoretical models is available in HTML and PDF formats. A paper describing the outcome of the Workshop on Archiving Structural Models of Biological Macromolecules will be available in the August 16 issue of Structure1.

Questions about this transition should be sent to info@wwpdb.org.

1.H.M. Berman, S.K. Burley, W. Chiu, A. Sali, A. Adzhubei, P.E. Bourne, S.H. Bryant, J. Roland L. Dunbrack, K. Fidelis, J. Frank, A. Godzik, K. Henrick, A. Joachimiak, B. Heymann, D. Jones, J.L. Markley, J. Moult, G.T. Montelione, C. Orengo, M.G. Rossmann, B. Rost, H. Saibil, T. Schwede, D.M. Standley, and J.D. Westbrook (2006) Outcome of a workshop on archiving structural models of biological macromolecules. Structure. 14: 1211-1217.

06/21/2006

wwPDB Statistics Available

Data from X-ray crystallographic, NMR, and cryo-electron microscopic experiments are deposited to the PDB archive by scientists from all over the world.

PDB data are processed by an international effort involving members of the wwPDB – the RCSB PDB, the Macromolecular Structure Database (MSD) at the EMBL's European Bioinformatics Institute, and Protein Data Bank Japan (PDBj). wwPDB annotators work with these data to make sure they are represented in the PDB archive in the best way possible. They run a series of checks, make corrections, and correspond with the depositors in an effort to make the data public as quickly and accurately as possible.

Statistics about the number of structures deposited, processed, and released by the wwPDB are available at Deposition Statistics.

04/27/2006

ADVISORY COMMITTEE MEETING

The second meeting of the world wide Protein Data Bank Advisory Committee (wwPDBAC) was held in Florence, Italy on August 30, 2005. The report of the meeting is available in PDF format.