Given a query protein structure, GIRAF searches for ligand binding sites in the PDB that are structurally similar to substructures of the query. As a query, you can specify a PDB ID or upload your own PDB-formatted file. For more information, please refer ...

On November 25, 2009, our existing data viewer xPSSS will be integrated into PDBj Mine, which has recently been developed. We started using our new data viewer, PDBj Mine, on Oct. 14, 2009. PDBj Mine uses RDB (PostgreSQL), while our exising xPSSS is ...

On October 22, 2009, PDBj main pages and deposition pages in " traditional Chinese " have been released.

On October 14, 2009, the weekly data update will be made, in principle, at 9:00 AM (JST) of every Wednesday, which corresponds to 0:00 (UTC). This update is simultaneously made at every member of the wwPDB: RCSB-PDB, PDBe, and PDBj. On October 14, 2009, ...

The changes to the wwPDB FTP site has been announced as "The advisory notice" at http://www.wwpdb.org/. (September 25, 2009)

PDB Archive Version 3.15 Released 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 ...

PDB Archive Version 3.15 to be Released March 18 , 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). ...

Directory structure in PDBj FTP site will be changed 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 ...

Announcement: PDB Archive Version 3.15 to be Released 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- ...

Announcement: New Releases to Follow Format Guide Version 3.20 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 ...

Comprehensive Format Guide Version 3.2 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 ...

The articles of "Molecule of the Month: MOM", which are produced by Dr. David S. Goodsell and appear at the RCSB-PDB Web pages, are translated into Japanese by the PDBj staff and are open here.

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 ...

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 ...

All new NMR depositions at the PDBj will use ADIT-NMR tool. New NMR deposition using ADIT is closed.

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/.

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.

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.

In xPSSS (xml-based Protein Structure Search Service), the XQuery search is available in addition to the current XPath search.

A new version of Structure Navigator-RT is provided so as to operate a Web service with the recent Grid technology: Opal-OP.

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.

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

Links to 3D-insight, GDB, KEGG are added to each result of the PDB browser (xPSSS).

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

XX CongressGeneral Assembly of the International Union of Crystallography - Florence 23 - 31 August 2005 - Find us as booth nos 2829 with our colleagues from the wwPDB. We will be running service demonstrations and be available for discussion throughout ...