Treatment of Theoretical Models in the Worldwide Protein Data Bank Archive

August 15, 2006

1. Introduction

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 macromolecules.

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.

2.0 Implementation Plan

2.1 Archiving of Current Models

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.

2.2 Archiving of Models after October 15, 2006

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.

2.3 Transition Plan (August 15-October 15, 2006)


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.