wwPDB 2012 News

16-March-2012

wwPDB Milestones: 80,000 Entries Released, PDB40 Meeting Report Published

The Archive Grows
With the March 13, 2012 update, 80,041 PDB entries became available in the archive. The PDB hit the 70,000 mark in December 2010.

In 2011, 8865 entries were deposited and annotated, while 8107 were released.

wwPDB deposition and download statistics are updated regularly.

Meeting Report
A review of the PDB40 meeting has been published:

The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley Structure (2012) 20: 391 - 396

Selected presentations and related details from the meeting are also available from http://www.wwpdb.org/PDB40.html.

6-March-2012

EM Data Bank joins the PDB archive

The EM Data Bank (EMDB), the primary archive for experimentally-determined maps obtained using three-dimensional electron microscopy methods, has joined the PDB archive (ftp://ftp.wwpdb.org), as announced previously.

The merger makes 3DEM results available in a single archive, including over 1300 electron microscopy derived maps from EMDB and 400 coordinates for EM map-derived models in PDB. It is also an essential step in the wwPDB's development of a Common Deposition & Annotation Tool that will cover all experimental methods, including hybrid methods.

With the addition of EMDB data, the physical size of the complete wwPDB archive jumps to roughly 180 GB (from its previous 130 GB). Sites that mirror the full wwPDB archive will need to increase storage capacity accordingly.

Summary information regarding the merger and detailed specifications for data access are posted at wwpdb.org/em/.

8-February-2012

A vision for validation of 3DEM maps and map-derived models

We are pleased to announce the publication of the outcome of the first Electron Microscopy Validation Task Force (EM VTF) meeting in the journal Structure: Henderson et al., Structure (2012).

The inaugural meeting of the EM VTF, organized by EMDataBank, Unified Data Resource for 3DEM, was held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. An international group of 3DEM experts explored how to assess maps, models, and other data that are deposited into the EM Data Bank (EMDB) and Protein Data Bank (PDB) public data archives. The 2-day workshop was co-chaired by Richard Henderson (MRC, Cambridge) and Andrej Sali (UCSF).

For deposited maps, the EM VTF recognized a critical need to develop standards for assessing map resolution and accuracy, and recommended reporting of map resolution in accordance with visible features, deposition of annotations specific to each map type, and validation of map symmetry.

For deposited map-derived models, EM VTF recommendations include establishment of criteria for assessing models both with and without regard to the fit to the map, creation of community-wide benchmarks for modelling methods, sequence annotation of all map components, and capability to archive coarse-grained representations of models.

Additional recommendations include establishing deposition guidelines for publication of 3DEM structures in journals, and expanding the role of EMDataBank to work together with the 3DEM community to provide unified access to 3DEM structures and to facilitate development of validation and data standards.

This initial report by the EM VTF follows closely on the heels of recommendations by the wwPDB X-ray VTF published last year (Structure, 2011 19: 1395-1412). Additional task forces have been convened for NMR and small angle scattering methods.

The efforts of all of the report authors are greatly appreciated: Richard Henderson, Andrej Sali, 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.

EMDataBank, Unified Data Resource for 3DEM (http://www.emdatabank.org), was established in 2007 and is a joint effort of the Protein Data Bank in Europe (PDBe) at the European Bioinformatics Institute, the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) at Rutgers, and the National Center for Macromolecular Imaging (NCMI) at Baylor College of Medicine, and is funded by the National Institutes of Health. EMDataBank serves the 3DEM and wider scientific communities with its 3DEM-specific portal for deposition and access to EM-derived structures and links to software, validation standards and conventions. The new report will serve as EMDataBank's roadmap for development of validation standards for data in 3DEM public data archivs in collaboration with the 3DEM community.

10-January-2012

Time-stamped Copies of the PDB Archive

A snapshot of the PDB archive (ftp.wwpdb.org) as of January 2, 2012 has been added to ftp://snapshots.wwpdb.org/. Snapshots have been archived annually since January 2005 to provide readily identifiable data sets for research on the PDB archive.

The directory 20120102 includes the 78,237 experimentally-determined coordinate files and related experimental data that were available at that time. Coordinate data are available in PDB, mmCIF, and XML formats. The date and time stamp of each file indicates the last time the file was modified.

The script at ftp://snapshots.wwpdb.org/rsyncSnapshots.sh may be used to make a local copy of a snapshot or sections of the snapshot.