wwPDB 2006 News
Contents
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.
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 [email protected].
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.