Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank
Spring 2012
Number 53


Data Deposition and Annotation

Volunteer Structures For Foldit

Foldit is an online game that attempts to predict the structure of a protein by taking advantage of humans' puzzle-solving intuitions and having people play competitively to fold the best proteins. Gamers use the Foldit interface to build protein models based upon the amino acid sequence.

ADIT depositors can submit their sequences to serve as puzzle challenges for the Foldit community. When submitting an entry to the PDB, select the following options in the Release Status category:

Depositions can also be considered as targets for CASD-NMR, CASP, FoldIt, and GPCR Dock.

  • Release status for coordinates: Hold for 8 weeks
  • Prerelease status for sequence information: Release Now
  • CASP/CASD/other method development target: Foldit
The deposition will appear as a Foldit Target in the Unreleased Structures search. Foldit will use the prereleased sequence as a puzzle, and gamers will be able to compare their predicted models to the experimental data when it is released 8 weeks later.

2012 Deposition Statistics

In the first quarter of 2012, 2470 experimentally-determined structures were deposited to the PDB archive.

82% were deposited with a release status of hold until publication; 14.6% were released as soon as annotation of the entry was complete; and 3.4% were held until a particular date. 93.0% of these entries were determined by X-ray crystallographic methods; 6.0% were determined by NMR methods.

Electron Microscopy Validation Task Force Report

To improve validation methods in the PDB, the wwPDB has convened method-specific Task Forces to collect recommendations and develop consensus on additional validation that should be performed, and to identify software applications to perform validation tasks.
The 2011 X-ray Validation Task Force report1 has been followed by the publication of Outcome of the First Electron Microscopy Validation Task Force Meeting in Structure (2012, 20:205-214).
At their 2010 inaugural meeting, this international group of 3DEM experts explored how to assess maps, models, and other data that are deposited into the EM Data Bank (EMDB) and PDB archives.

Many thanks to the authors and meeting participants: Richard Henderson (Co-chair, map validation), Andrej Sali (Co-chair, model validation), Matthew L. Baker, Bridget Carragher, Batsal Devkota, Kenneth H. Downing, Edward H. Egelman, Zukang Feng, Joachim Frank, Nikolaus Grigorieff, Wen Jiang, Steven J. Ludtke, Ohad Medalia, Pawel A. Penczek, Peter B. Rosenthal, Michael G. Rossmann, Michael F. Schmid, Gunnar F. Schröder, Alasdair C. Steven, David L. Stokes, John D. Westbrook, Willy Wriggers, Huanwang Yang, Jasmine Young, Helen M. Berman, Wah Chiu, Gerard J. Kleywegt, and Catherine L. Lawson.

1. A new generation of crystallographic validation tools for the Protein Data Bank. R.J. Read, P.D. Adams, W.B. Arendall III, A.T. Brunger, P. Emsley, R.P. Joosten, G.J. Kleywegt, E.B. Krissinel, T. Lutteke, Z. Otwinowski, A. Perrakis, J.S. Richardson, W.H. Sheffler, J.L. Smith, I.J. Tickle, G. Vriend, P.H. Zwart (2011) Structure 19: 1395-1412. doi:10.1016/j.str.2011.08.006