News (on 19 Aug., 2010):

Validation Report PDFs

wwPDB members provide depositors with detailed reports that include the results of geometric and experimental data checking as part of the structure annotation process. These documents are available from all wwPDB annotation sites as PDF files so that they may be easily reviewed and shared by depositors.

As these PDB validation reports provide an assessment of structure quality while keeping the coordinate file confidential, we encourage journal editors and referees to request them from depositors as part of the manuscript submission and review process. The reports are date-stamped, and display the wwPDB processing site logo. They contain essentially the same information, regardless of PDB annotation site (Example reports: RCSB PDB | PDBe | PDBj). The validation reports will continue to be developed and improved as we receive recommendations from our Validation Task Forces for X-ray, NMR, EM, and small angle scattering methods, and as we further develop our data deposition and processing procedures.

PDB validation reports are already required by the International Union of Crystallography (IUCr) journals as part of their submission process and are described in an editorial recently published in Nature Structural & Molecular Biology.

Questions about these reports and the annotation process may be sent to PDBj or info@wwpdb.org.

News (on 13 Jul., 2010):
The latest version of jV (jV3.8), the molecular graphics viewer developed by PDBj, has been released. A new functional command "displayatom on/off" has been added, which provides various display methods easily. Please download the newest version from here.

News (on 13 Jun., 2010):
Version 2 NMR restrain files have been released.

News (on 19 May., 2010):
The latest version of jV (jV3.7.1) has been released.

News (on 7 May., 2010):
The IP address of PDBj ftp server (ftp.pdbj.org) has been changed to 133.1.158.142. If you access to the PDBj ftp using the IP address directly, please replace the IP address with the new one. The IP address of PDBj Web server has also been changed. You do not need to make any change when accessing with the host name.

News (on 6 May., 2010):

wwPDB To Provide Validation Reports as PDFs

As part of the structure annotation process, wwPDB members provide depositors with detailed reports that include the results of geometric and experimental data checking. Beginning May 17, 2010 these documents will be available from all wwPDB annotation sites as PDF files so that they may be easily reviewed and shared by depositors.

As these PDB validation reports provide an assessment of structure quality while keeping the coordinate file confidential, we encourage journal editors and referees to request them from depositors as part of the manuscript submission and review process. PDB validation reports are already required by the International Union of Crystallography (IUCr) journals as part of their submission process (see Baker et al. (2010) Acta Cryst. F66: 112). The reports are date-stamped, and display the wwPDB processing site logo. They contain essentially the same information, regardless of PDB annotation site. The validation reports will continue to be developed and improved as we receive recommendations from our Validation Task Forces for X-ray, NMR, EM, and small angle scattering methods, and as we further develop our data deposition and processing procedures.

Questions about these reports and the annotation process may be sent to us or info@wwpdb.org.

News (on 6 May., 2010):

Version 2 NMR Restraint Files to be Released in the wwPDB FTP on June 30, 2010

With the June 30, 2010 update, a new set of NMR restraint data files will be added to the wwPDB FTP archive (ftp://ftp.wwpdb.org, ftp://ftp.ebi.ac.uk, and ftp://pdb.protein.osaka-u.ac.jp). These restraint files, which will be identified as Version 2 files, are represented in NMR-STAR 3.1 format, contain current PDB atom nomenclature, and provide accurate atom-level correspondences to the NMR model coordinate files in the current wwPDB archive. Restraint files containing restraint data as originally deposited (Version 1 files) will remain on the site and will continue to be updated regularly as new NMR entries are released.

About Version 2 Restraint Files

The Version 2 NMR restraint files were generated for the wwPDB by the BMRB in collaboration with PDBe and the Centre for Molecular and Biomolecular Informatics/Institute for Molecules and Materials at the Radboud University Nijmegen.

NMR restraints were parsed from their original format (Version 1), and harmonized with the coordinates using the software packages Wattos (BMRB and CMBI/IMM), FormatConverter and NMRStarExport (PDBe), and the CCPN framework.

The complexity of this process may have lead to minor modifications or loss of data in the Version 2 restraint files due to parsing or conversion errors. The PDB coordinate file and the Version 1 restraint files remain the primary reference for these data.

More information about the process used to generate these files is available (1-3).

Changes to wwPDB FTP Server

The initial release of the Version 2 NMR restraint files will add approximately 5625 new files (310 Mbytes) to the wwPDB FTP site. Version 2 restraint files for new PDB entries will be processed and made available after the PDB entry has been released. Version 1 restraint files for new PDB entries will continue to be released weekly.

NMR restraint files are named using extension .mr, as in "1abc.mr.gz" for PDB ID 1abc. Version 2 restraint files will be named "1abc_mr.str.gz", where "str" identifies the NMR-STAR (V3.1) data format. All restraint files are compressed (.gz) using the GNU gzip program.

Version 2 restraint files will be stored in a new directory path, grouped by the middle two characters of the 4-character PDB ID:
ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/data/structures/divided/nmr_restraints_v2/

All of these data files will be symbolically linked to a single directory:
ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/data/structures/all/nmr_restraints_v2/

Version 1 restraint files will remain in their current directory structure.

For questions, please contact us or info@wwpdb.org.

References

1. JF Doreleijers, A Nederveen, W Vranken, J Lin, AM Bonvin, R Kaptein, JL Markley, and EL Ulrich (2005). BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J. Biomol. NMR 32, 1-12.
2. WF Vranken, W Boucher, TJ Stevens, RH Fogh, A Pajon, M Llinas, EL Ulrich, JL Markley, J Ionides, and ED Laue (2005). The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59, 687-696.
3. JF Doreleijers, WF Vranken, C Schulte, J Lin, JR Wedell, CJ Penkett, GW Vuister, G Vriend, JL Markley, and EL Ulrich (2009). The NMR Restraints Grid at BMRB for 5,266 Protein and Nucleic Acid PDB Entries. J Biomol. NMR 45, 389-396.

News (on 24 Nov., 2009):
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 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.
Since PDBj Mine is a relational database and cannnot perform a search using XQuery or XPath, xPSSS will still be available, only for the purpose, at http://service.pdbj.org/xPSSS/.

News (on 22 Oct., 2009):
On October 22, 2009, PDBj main pages and deposition pages in "traditional Chinese" have been released.

News (on 9 Oct., 2009):
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.

News (on 9 Oct., 2009):
On October 14, 2009, we will start to use a new data viewer, PDBj Mine, which has been recently developed by PDBj. Because PDBj Mine uses a relational database, XPath/XQuery is not available. Our XML-based database, xPSSS, is still available for another couple of months.

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

News (on 18 Mar., 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 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):
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).

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):
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 decided to remove it and will change the directory structure in PDBj FTP as follows:

Before

Current PDB archive

ftp://pdb.protein.osaka-u.ac.jp/v3/pub/pdb/

20070731 snapshot (the latest release before remediation)

ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/

After 2009-01-27

Current PDB archive

ftp://pdb.protein.osaka-u.ac.jp/v3/pub/pdb/

20070731 snapshot (the latest release before remediation)

ftp://pdbjsnap.protein.osaka-u.ac.jp/20070731/

And we will reconstruct as the following after the version 3.15 PDB archive will be released:

The version 3.15 PDB archive

ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/

20070731 snapshot (the latest release before remediation)

ftp://pdbjsnap.protein.osaka-u.ac.jp/20070731/

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):
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-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):
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 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):
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 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):
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.

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), 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.

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).