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PDBj (Protein Data Bank Japan) maintains a centralized archive of macromolecular structures and provides integrated tools, in collaboration with the RCSB, the BMRB in USA and the PDBe in EU. PDBj is supported by JST-BIRD.
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News (on 24 Nov., 2009): We started using our new data viewer, PDBj Mine, on Oct. 14, 2009. PDBj Mine uses RDB (PostgreSQL), while our exising xPSSS is native XML-based database.
After 9 a.m. Nov.25, 2009, all the accesses to the exising data viewer xPSSS will be automatically switched to jump to PDBj Mine. News (on 22 Oct., 2009): News (on 9 Oct., 2009): News (on 9 Oct., 2009): News (on 25 Sep., 2009): News (on 18 Mar., 2009): A newly standardized and enhanced version of the entire PDB archive at ftp://ftp.protein.osaka-u.ac.jp/ and 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 www.wwpdb.org/docs.html. A time-stamped snapshot of the PDB archive before this release is available from ftp://pdbjsnap.protein.osaka-u.ac.jp/ and 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 “PDBj PDB Archive/Snapshot Archive” or http://www.wwpdb.org/downloads.html. For users who make local copies of the wwPDB FTP from PDBj FTP site, please see also News on 2009-01-23. 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 us or info@wwpdb.org. News (on 13 Feb., 2009): The wwPDB will release a newly standardized and enhanced version of the entire PDB archive at ftp://ftp.protein.osaka-u.ac.jp/ and ftp://ftp.wwpdb.org with the March 18, 2009 update (Japan time). 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 www.wwpdb.org/docs.html. A time-stamped snapshot of the PDB archive before this release will be available from ftp://pdbjsnap.protein.osaka-u.ac.jp/ and 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 “PDBj PDB Archive/Snapshot Archive” or http://www.wwpdb.org/downloads.html. For users who make local copies of the wwPDB FTP from PDBj FTP site, please see also News on 2009-01-23. 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. News (on 23 Jan., 2009): As we described in the “Download” page, PDBj produces the 20070731 snapshot which is the latest release before the remediation was applied. It is now available from the PDBj snapshot archive. So, we have decided to remove it and will change the directory structure in PDBj FTP as follows: Before
After 2009-01-27
And we will reconstruct as the following after the version 3.15 PDB archive will be released:
We will keep ftp://pdb.protein.osaka-u.ac.jp/v3/ as a symbolic link to (updated) ftp://pdb.protein.osaka-u.ac.jp/ in the meantime. But we encourage you to update your services/software to the new directory structure AFTER the change. We will announce the release date for version 3.15 PDB archive when it will be confirmed. Sorry for your inconvenience and thank you for your kind understanding. News (on 8 Dec., 2008): A new standardized version of the PDB archive will be available from ftp://ftp.protein.osaka-u.ac.jp/ and ftp://ftp.wwpdb.org in early 2009. 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://pdbjsnap.protein.osaka-u.ac.jp/ and ftp://snapshots.wwpdb.org/. For documentation, please see www.wwpdb.org/docs.html. Questions may be sent to info@wwpdb.org. News (on 25 Nov., 2008): Beginning December 2, 2008, all newly-released PDB entries will follow PDB File Format Contents Guide Version 3.20 (PDF | HTML). This format includes site and assembly annotation, and supports the nomenclature introduced in 2007 in the Chemical Component Dictionary. The Version 3.20 Changes Guide (PDF) highlights the changes in format from 3.1. Please send any questions to info@wwpdb.org. News (on 16 Sep., 2008): During the past year, the wwPDB annotators have collaborated on a project to clarify the details and procedures related to data processing and annotation. The result is a PDB Contents Guide Version 3.2 that more fully describes the PDB file format. This document is available as a PDF and in HTML, and is accompanied by a document highlighting these clarifications. In the coming months, all files released by the wwPDB will follow the format as described in this document. Details will be made available on this website and at www.wwpdb.org.
News (on 2 Apr., 2008): Data download service via rsync is started. We have started to provide remediated PDB archive via rsync protocol. Rsync is a software which synchronizes files and directories from one location to another while minimizing data transfer using delta encoding when appropriate. Detailed information for PDB archive service is available from PDB archive web page.
News (on 12 Dec., 2007): These data must be deposited at a member site of the Worldwide Protein Data Bank (www.wwpdb.org): PDBj (www.pdbj.org), RCSB PDB (www.pdb.org), PDBe (www.ebi.ac.uk/msd), or BMRB (www.bmrb.wisc.edu). Data can be released as soon as they have been processed and approved. There is a one-year limit on the length of time a structure and its experimental data can be put on hold, including structures that are on hold until the associated paper is published (HPUB). This policy was developed as a result of comments and recommendations from the PDB user community, including the Commission on Biological Macromolecules of the International Union of Crystallography and the NMR Task Force, and has been endorsed by the wwPDB Advisory Committee.
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