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Our XML-based browser, xPSSS, has been revised, so that the previous Theoretical models are searched and downloaded.

We start a new service, Sequence Navigator, to allow searching for homologous proteins using the amino acid sequence.

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.

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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.

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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 ...

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

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

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

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.

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

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

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.

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 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/.

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

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 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 ...

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.

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 ...

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 ...

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- ...