Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank

Spring 2009
Number 41

 
NEWSLETTER
  Contents  
Home | Newsletter Archive | PDF Version
Message from the RCSB PDB
Data Deposition
PDB Archive Version 3.15 Released
Papers Published
Deposition Statistics
Data Query, Reporting and Access
Website Statistics
New Feature: Receive Email Alerts When New Structures Match Your Queries with MyPDB
Time-stamped Copies of PDB Archive Available via FTP
Outreach and Education
New Jersey Science Olympiad: Protein Modeling
Education Corner
Gavin Whittaker, Ph.D.,
Molecular Models: Tangible Representations of the Abstract
PDB Community Focus
GaŽl McGill, Ph.D., and Graham Johnson, Molecular Animators
RCSB PDB PARTNERS, MANAGEMENT, AND STATEMENT OF SUPPORT
 
     

DATA DEPOSITION

PDB Archive Version 3.15 Released

A new standardized version of the PDB archive will be available from ftp://ftp.wwpdb.org in early 2009. The date will be announced at wwpdb.org.

As of December 2, 2008, all new PDB releases follow PDB File Format Contents Guide Version 3.20. With the new version of the archive, all entries released prior to December 2, 2008 will be re-released as PDB Format Version 3.15 files. This release will overwrite all existing files.

A snapshot of the archive before this release will be available from ftp://snapshots.wwpdb.org/. Tools for downloading the archive can be found at www.wwpdb.org/downloads.html. For file format documentation, please see www.wwpdb.org/docs.html.

Questions may be sent to info@wwpdb.org.


Papers Published

Recently published papers describe the wwPDB collaboration and data formats. Other RCSB PDB publications are listed at the RCSB PDB website. Reprints may be requested by contacting info@rcsb.org.

  • The PDB format, mmCIF formats, and other data formats (2009) in Structural Bioinformatics, second edition, P. Bourne and J. Gu, eds. Hoboken, NJ, John Wiley & Sons, Inc. pages 271-291.
  • The Worldwide Protein Data Bank (2009) in Structural Bioinformatics, second edition, P. Bourne and J. Gu, eds. Hoboken, NJ, John Wiley & Sons, Inc. pages 293-303.
  • Data Deposition and Annotation at the Worldwide Protein Data Bank Molecular Biotechnology (2008) [ doi: 10.1007/s12033-008-9127-7 ].

Deposition Statistics

In the first quarter of 2009, 2041 experimentally-determined structures were deposited to the PDB archive. The entries were processed by wwPDB teams at the RCSB PDB, PDBe, and PDBj.

Of the structures deposited, 75.9% were deposited with a release status of "hold until publication"; 21.2% were released as soon as annotation of the entry was complete; and 2.9% were held until a particular date. 90.9% of these entries were determined by X-ray crystallographic methods; 8.5% were determined by NMR methods.

During the same time period, 1712 structures were released in the PDB.

 
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