The PDB Archive download service is now available via the http protocol in addition to ftp and rsync.

• http://ftp.pdbj.org/ (current main PDB Archive)
• http://ftp-versioned.pdbj.org/ (versioned PDB Archive)

＊Please see also "About contents in PDBj FTP site" help page for details.

http://onlinelibrary.wiley.com/doi/10.1002/pro.3273/full

New tools and functions in Data-out activities at Protein Data Bank Japan (PDBj)
Kinjo, A.R., Bekker, G.-J., Wako, H., Endo, S., Tsuchiya, Y., Sato, H., Nishi, H., Kinoshita, K., Suzuki, H., Kawabata, T., Yokochi, M., Iwata, T., Kobayashi, N., Fujiwara, T., Kurisu, G. and Nakamura, H.
Protein Science 27 (1): 95-102 (2018)

The new version includes Chemical Component(cc), Chemical Component Model(ccmodel) and BIRD molecule(prd) schema. The schema of the PDBj Mine 2 RDB has also been upgraded to pdbx-v50-v5.287.
Please download the dump files for the new cc, ccmodel and prd. The delta files will be available from next week. Please also refer to RDB help page.

Overview of PDB Validation Reports published in Structure (wwPDB news)

Individual Chemical Component Dictionary files (in mmCIF and PDBML) are now available at PDBj's FTP archive.
For more details, please try Chemie search and chem_comp/RDF service.

Science Agora 2017 －in Tokyo－

Science Agora is a generic term for a place connecting science and society, which is open to everyone. People gathering in this forum will aim to realize “science harmonized with society” and a “society harmonized with science” through dialogue and collaboration while respecting a diversity of values.

Date：

• November 24 (Friday), 2017 (13:30〜18:00)
• November 25 (Saturday) - November 26 (Sunday) (10:00〜16:00)

Venues：

Telecom Center Building, Odaiba Tokyo

5th floor Area D (innovating new knowledge by linking different fields), Booth No.65

"Shape" of proteins, which supporting the life

1. "Watching" by accessing PDBj database and browsing protein molecules with CG in sterically.
2. "Feeling" by touching the molecule models made with a 3D printer
3. "Constructing" by making molecules with paper crafts

Implementation of PDB Entry Versioning and Better Revision History to Improve PDB Archive Management (wwPDB news)

The wwPDB Foundation raises funds from Individual and Corporate sponsors in support of the outreach activities of the wwPDB crucial to the future of the PDB archive, including workshops, symposia, and advisory meetings.

See the wwPDB news for more details.

＜PDBj luncheon seminar＞

PDBj luncheon seminar will be held at The 55TH ANNUAL MEETING OF THE BIOPHYSICAL SOCIETY OF JAPAN .

Date	September 21 (Thu), 2017 11：45－12：35
Place	Kurokami North Campus, Kumamoto University Room I （Room E305 , General Education Bldg. 3F）
number of seats	100

<Presenter・Title>

• Genji KURISU (Institute for Protein Research (IPR), Osaka University)
  "Recent activities of PDBj and wwPDB"
• Akira KINJO (Institute for Protein Research (IPR), Osaka University)
  "Querying the PDBj Mine2 relational database"
• Hirofumi SUZUKI (Institute for Protein Research (IPR), Osaka University)
  "Situation, utilization and visualization of cryo-EM structure data"

※ Please take a numbered ticket (first come, first served) ahead at the reception counter on the day.

• seminar summary（pdf 1.8MB）
• program（pdf 3.8MB）

PDB-Dev: A Prototype System for Integrative/Hybrid Structural Models announced in Structure (wwPDB News)

Poster Prize Awarded at IUCr 2017 (wwPDB News)

PDBx/mmCIF Conversion service provided by PDBj now supports Chemical Component files in mmCIF format. The Chem Comp file in mmCIF format is converted to PDB format file.

wwPDB Events at IUCr (August 21-28) (wwPDB News)

Better Management of PDB Archive with File Versioning and Revision History (wwPDB News)

PDBj has launched the JBI (Japan alliance for Bioscience Information) portal site (http://jbioinfo.jp/) in collaboration with National Bioscience Database Center (NBDC)/JST, Database Center for Life Science (DBCLS)/Joint Support-Center for Data Science Research/ROIS, DNA Data Bank of Japan (DDBJ)/National Institute of Genetics/ROIS. This portal site provides one-stop service of databases and tools which are helpful in various scenes of the life science research.
Visit the website (http://jbioinfo.jp/) for more detail.

5 Easy Steps to PDB Deposition (wwPDB News)

Freezing the PDB Format (wwPDB News)

Enriched PDB Structure Entry Files Conforming to OneDep Data Standards Are Now Available for Testing (wwPDB News)

Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive (wwPDB News)

Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive (wwPDB News)

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Impact on PDBj services

Mine2 RDB was upgraded to pdbx-v50-v5.282.
Please refer to the past news regarding impact of V5.0 upgrade on PDBj services.

On July 12 2017, the PDB entries in the FTP will be upgraded to the new v5 dictionary ( http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) (wwPDB News). Since this will be a major upgrade, some services will be affected. The following services will be affected by this upgrade:

Mine 2 RDB

Because all entries have been modified, the weekly delta file would be huge and will for that reason NOT be provided on the 12th. The delta files from the previous weeks will also no longer be included on the FTP. Delta files will be included again in the following week onwards (19th). Users will have to delete the current contents of the RDB and then download and load the full dump file, as described on the RDB help page.

Legacy PDBj Mine

Legacy PDBj Mine will no longer be updated after the transition of the PDBx/mmCIF dictionary from version 4 (v4) to version 5 (v5) planned on July 12, 2017. After this date, please use the new interface for PDBj Mine that will be compatible with the v5 data. The legacy PDBj Mine will be closed at the end of August, 2017.

Archival PDBx/mmCIF Version V4 to V5 Update in the Protein Data Bank (wwPDB News)

Updated Validation Reports for Archived PDB Structures Now Available (wwPDB News)

Data Management: A global coalition to sustain core data (wwPDB News)

The paper describing wwPDB OneDep system is now available (wwPDB News)

Time-stamped Copies of the PDB Archive Available (wwPDB News)