On November 19-20, 2005, a workshop was held at the RCSB Protein Data Bank in
Rutgers University to discuss the archiving of theoretical models. It was attended by a
cross-section of the structural biology community including modelers, cryo-electron
microscopists and structural genomicists as well as representatives of wwPDB. The
outcome of this workshop was a set of recommendations and implementation plans. The
key recommendation is:
PDB depositions should be restricted to atomic coordinates that are substantially
determined by experimental measurements on specimens containing biological
This includes, for example, structures determined by X-ray crystallography, NMR and
cryo-electron microscopy. It does not include models determined purely in silico using,
for example, homology or ab initio methods. A paper describing the outcome of the
Workshop on Archiving Structural Models of Biological Macromolecules available in the
August 16 issue of Structure 1.
At the request of the PDB Advisory Committee, an
implementation plan was written. The plan outlined below has been reviewed and
approved by that body and the wwPDBAC.
Theoretical models that have been previously released or that are released under the
provisions of the transition process described below will continue to be made publicly
available only via the existing models archive, which is maintained as a distinct and
separate archive from that for experimental structures.
Archiving of theoretical models will be phased out such that theoretical model depositions
will no longer be accepted after October 15, 2006. On October 15, the theoretical model
deposition views on all wwPDB deposition servers will be removed.
All existing un-processed theoretical model entries as well as entries deposited
from August 15 through October 15, 2006 will not be validated and will not be
processed. The PDB format file will be generated only from the information the author
supplied during deposition and the entry will be released as-is without author review or
corrections. The authors will have the choice of correcting their entries by withdrawing
the original entry and then re-submitting the corrected version before October 15, 2006.
The details of this implementation are:
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) Archiving structural models of biological macromolecules:
outcome of a workshop on biological macromolecular structure models.
Structure. 14: 1211-1217.
RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.