News (on 20 Dec., 2007):
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):
Effective February 1, 2008, structure factor amplitudes/intensities (for crystal structures) and restraints (for NMR structures) will be a mandatory requirement for PDB deposition.

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), MSD-EBI (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.

News (on 1 Nov., 2007):
All new NMR depositions at the PDBj will use ADIT-NMR tool. New NMR deposition using ADIT is closed.

News (on 1 Aug., 2007):
The PDB archive has been remediated and is available starting August 1, 2007 from ftp://ftp.wwpdb.org/ and from our mirror site: ftp://pdb.protein.osaka-u.ac.jp/v3/.

News (on 21 May., 2007):
PDBj has started the following two new services:
EM Navigator, a browser for searching the electron microscopy structures and XQuad (XQuery Advisor), a advisory tool for creating XQuery for searching the PDB data.

News (on 25 Apr., 2007):
The wwPDB (www.wwpdb.org) has collaborated on a project to remediate the PDB archive and create a new set of corrected files, the test data of which are now released.

News (on 18 Oct., 2006):
In xPSSS (xml-based Protein Structure Search Service), the XQuery search is available in addition to the current XPath search.

News (on 14 Oct., 2006):
A new version of Structure Navigator-RT is provided so as to operate a Web service with the recent Grid technology: Opal-OP.

News (on 11 Aug., 2006):
To theoretical model depositors, the wwPDB (PDBj, RCSB, EBI) annotation groups change the policy of accepting and processing theoretical model structures on August 15, 2006. Please see the details.

News (on 21 Apr., 2006):
We have relaunched our website on April 21 (Friday) , 2006 (Japanese time).

News (on 27 Feb., 2006):
Links to 3D-insight, GDB, KEGG are added to each result of the PDB browser (xPSSS).

News (on 28 Dec., 2005):
RCSB-PDB mirror site in Osaka University, Japan is closed on Dec 28, 2005 (Japanese time). Please access PDBj site from now on.

News (on 21 Jun., 2005):
XX Congress & General Assembly of the International Union of Crystallography - Florence 23 - 31 August 2005
- Find us as booth nos 28 & 29 with our colleagues from the wwPDB. We will be running service demonstrations and be available for discussion throughout the exhibition.

News (on 28 Apr., 2005):
The data, text, and figures on this site are free to the public. When you make use of the contents of this site, please cite as "Protein Data Bank japan: PDBj".
The ftp archival site is provided at ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/ .

News (on 10 Dec., 2004):
PDBj starts the following two new services:
Structure Navigator, a tool for querying the PDB using structure similarity, and GASH, a robust structure alignment program.

News (on 16 Nov., 2004):
We release the latest version of PDBjViewer, jV3, which can be used both as applet and stand alone on windows 2000/XP, Macintosh OS-X, and Linux.

News (on 12 Nov., 2004):
PDBj starts a new service in xPSSS to display the Electron Density Map of each biological macromolecule, whose structure factor file has been deposited, through the Summary page or the Experimental Details page of xPSSS.

News (on September 1, 2004) :
We start a new service, Sequence Navigator, to allow searching for homologous proteins using the amino acid sequence.

News (on July 30, 2004) :
Our XML-based browser, xPSSS, has been revised, so that the previous Theoretical models are searched and downloaded.

News (on June 23, 2004) :
Functional Details Page has been revised for each result of the PDB browser(xPSSS), so that the correct chain names appear.

News (on April 13, 2004) :
Functional Details Page is added in each result of the PDB browser (xPSSS).