wwPDB 2009 News

Contents

12/16/2009 Coordinated wwPDB Release of Data
09/25/2009 wwPDB FTP Advisory Notice
06/30/2009 wwPDB News: Gerard Kleywegt to head Protein Data Bank Europe
03/17/2009 PDB Archive Version 3.15 Released
03/10/2009 Announcement: PDB Archive Version 3.15 to be Released March 17, 2009*
02/11/2009 Announcement: PDB Archive Version 3.15 to be Released March 2009
01/28/2009 wwPDB Paper: Deposition and Annotation
01/20/2009 Time-stamped Copies of PDB Archive Available via FTP
12/18/2008 Advisory Committee Meeting

12/16/2009

Coordinated wwPDB Release of Data

The PDB archive can be accessed at FTP sites at the RCSB PDB, PDBe, and PDBj. The update schedules for these sites have been coordinated to be simultaneous. All updates now occur at the target time of Wednesday 00:00 UTC (Coordinated Universal Time).

There is no change to the timeline for structure release requests. Any author correspondence required to release a PDB entry should be sent to the appropriate wwPDB member site by 12 noon local time on Thursdays in order for the entry to be prepared for release. This correspondence (which can include citation information, responses to outstanding issues, etc.) should be sent to:

After the files are ready, all entries due for release are transferred to the RCSB PDB for final packaging into the master PDB ftp archive. These files are then released by at the target time of Wednesday, 00:00 UTC (Coordinated Universal Time).

Requests received after these cutoff times will be processed during the next update cycle.

09/25/2009

wwPDB FTP Advisory Notice

This advisory notice describes four changes to the content of the wwPDB FTP site. The changes described here will become effective on Nov 24, 2009.

  1. The script for mirroring the FTP site using the RSYNC program has been updated. The new script has been modified to prompt the user to choose one of three rsync servers (RCSB PDB, PDBe, PDBj). The rsync script has the following URLs:

    RCSB PDB: ftp://ftp.wwpdb.org/pub/pdb/software/rsyncPDB.sh
    PDBe: ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/software/rsyncPDB.sh
    PDBj: ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/software/rsyncPDB.sh

  2. The top-level README file has been updated to point to an expanded set of download instructions hosted on the wwPDB website. The URL for the download instructions is:

    wwPDB website: Download Archive - Data Download Instructions

    The URLs for the updated README file are located at:

    RCSB PDB: ftp://ftp.wwpdb.org/pub/pdb/README
    PDBe: ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/README
    PDBj: ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/README

  3. The directories containing newsletters have been updated. Newsletters can be found in the following URLs:

    RCSB PDB: ftp://ftp.wwpdb.org/pub/pdb/doc/newsletters/
    PDBe: ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/doc/newsletters/
    PDBj: ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/doc/newsletters/

  4. Sequence cluster data that is used only by the RCSB PDB website has been relocated to an RCSB PDB resource site. This data was formerly located at the following URLS:

    RCSB PDB: ftp://ftp.wwpdb.org/pub/pdb/derived_data/NR/
    PDBe: ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/derived_data/NR/
    PDBj: ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/derived_data/NR/

The new URL for this data is:

RCSB PDB: ftp://resources.rcsb.org/sequence/clusters/

06/30/2009

wwPDB News: Gerard Kleywegt to head Protein Data Bank Europe

Starting July 1, 2009, Gerard Kleywegt will lead the Protein Data Bank Europe (PDBe) project at the European Bioinformatics Institute (Hinxton, UK). During the last 17 years he has been working in Uppsala, Sweden, a center of excellence for biomolecular crystallography and has developed many tools that are widely used by structural biologists worldwide. He has an extensive publication record and has served on the PDBe Scientific Advisory Board for the last few years. He has also been one of the European representatives on the wwPDB advisory committee. He has a very strong international reputation and is well respected in the structural biology community.

Gerard will be replacing Kim Henrick, who has been the team leader of the PDBe since 2001. During his tenure at the EBI, Kim has made enormous contributions to the PDBe at the EBI, by establishing and leading a strong team that has developed a wide variety of services. Kim was a strong advocate for the formation of the wwPDB in 2003. He has played a key role in developing the standards for representing all the data in the archive from small molecules to very large biological assemblies, and in leading the remediation efforts. Kim's deep knowledge of the PDB, his very critical eye, and sharp wit will be greatly missed by the wwPDB.

The members of the wwPDB look forward to working closely with Gerard and wish Kim all the best in the next chapter of his career.

03/17/2009

PDB Archive Version 3.15 Released

A newly standardized and enhanced version of the entire PDB archive at ftp://ftp.wwpdb.org has been released.

Files originally released before December 2, 2008 will follow PDB Format Version 3.15; files originally released after that date will follow Version 3.20. For detailed file format documentation, please see File Format Documentation.

A time-stamped snapshot of the PDB archive before this release is available from ftp://snapshots.wwpdb.org/ in the directory 20090316.

Users who maintain local copies of the wwPDB FTP will have to download the entire archive. Scripts to help in this process are available at Download Archive - Data Download Instructions.

These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users worldwide. This release includes improvements and enhancements to the data, including details about the chemistry of the polymer and the ligands bound to it, biological assemblies, and binding sites of ligands and metal ions. An overview (PDF) is provided at the wwPDB website.

Questions may be sent to info@wwpdb.org.

03/10/2009

Announcement: PDB Archive Version 3.15 to be Released March 17, 2009*

The wwPDB will release a newly standardized and enhanced version of the entire PDB archive at ftp://ftp.wwpdb.org with the March 17, 2009 update. *Please note the revised date.

Files originally released before December 2, 2008 will follow PDB Format Version 3.15; files originally released after that date will follow Version 3.20. For detailed file format documentation, please see File Format Documentation.

A time-stamped snapshot of the PDB archive before this release will be available from ftp://snapshots.wwpdb.org/.

Users who maintain local copies of the wwPDB FTP will have to download the entire archive. Scripts to help in this process are available at Download Archive - Data Download Instructions.

These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users worldwide.

Questions may be sent to info@wwpdb.org.

02/11/2009

Announcement: PDB Archive Version 3.15 to be Released March 2009

The wwPDB will release a newly standardized and enhanced version of the entire PDB archive at ftp://ftp.wwpdb.org in March 2009.

Files originally released before December 2, 2008 will follow PDB Format Version 3.15; files originally released after that date will follow Version 3.20. For detailed file format documentation, please see File Format Documentation.

A time-stamped snapshot of the PDB archive before this release will be available from ftp://snapshots.wwpdb.org/.

Users who maintain local copies of the wwPDB FTP will have to download the entire archive. Scripts to help in this process are available at Download Archive - Data Download Instructions.

These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users worldwide.

Questions may be sent to info@wwpdb.org.

01/28/2009

wwPDB Paper: Deposition and Annotation

wwPDB deposition tools, methods, and policies have been described in

Data Deposition and Annotation at the Worldwide Protein Data Bank Molecular Biotechnology (2008) [ doi:10.1107/S0907444908017393 ]
Shuchismita Dutta, Kyle Burkhardt, Jasmine Young, Ganesh J. Swaminathan, Takanori Matsuura, Kim Henrick, Haruki Nakamura and Helen M. Berman

01/20/2009

Time-stamped Copies of PDB Archive Available via FTP

A time-stamped snapshot of the PDB archive (ftp://ftp.wwpdb.org) as of January 5, 2009 has been added to ftp://snapshots.rcsb.org/. Snapshots of the PDB have been archived annually since 2004. It is hoped that these snapshots will provide readily identifiable data sets for research on the PDB archive.

The script at ftp://snapshots.rcsb.org/rsyncSnapshots.sh may be used to make a local copy of a snapshot or sections of the snapshot. The directory 20090105 includes the 55,072 experimentally-determined coordinate files that were current 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.

12/18/2008

Advisory Committee Meeting

The Worldwide Protein Data Bank Advisory Committee (wwPDBAC) met in Hinxton on September 29, 2008. The presentations by wwPDB members and the report from the wwPDBAC are available at wwPDB Advisory Committee Meetings.