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

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

2017-12-21
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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)

2017-12-19
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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.
2017-12-06
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Overview of PDB Validation Reports published in Structure (wwPDB news)
2017-12-02 (last edited: 1 month ago)2017-12-05
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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.
2017-11-22
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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

(The website linked from the title is displayed only in Japanese)
The aim of our exhibition is providing chances for various people to realize the diversity and importance of the "Shape" of proteins though experiences such as watching, feeling and constructing. We hope it helps them to deepen their understanding for biomolecules. The details of exhibition are as following:
  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
We also introduce the methods and facilities such as synchrotrons and high resolution electron microscopes (Nobel Prize of this year was awarded for it!) to solve molecule shapes.
2017-11-16 (last edited: 3 months ago)2017-11-17
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Implementation of PDB Entry Versioning and Better Revision History to Improve PDB Archive Management (wwPDB news)

2017-10-05 (last edited: 4 months ago)2017-10-05
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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.
2017-09-26
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<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.

2017-09-19 (last edited: 4 months ago)2017-09-22
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PDB-Dev: A Prototype System for Integrative/Hybrid Structural Models announced in Structure (wwPDB News)
2017-09-08
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Poster Prize Awarded at IUCr 2017 (wwPDB News)
2017-08-31
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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.
2017-08-22 (last edited: 5 months ago)2017-08-22
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wwPDB Events at IUCr (August 21-28) (wwPDB News)
2017-08-21 (last edited: 5 months ago)2017-08-21
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Better Management of PDB Archive with File Versioning and Revision History (wwPDB News)
2017-08-02 (last edited: 6 months ago)2017-08-03
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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.
2017-07-14
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Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive (wwPDB News)

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.
2017-07-12 (last edited: 6 months ago)2017-07-31
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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.
2017-06-21 (last edited: 6 months ago)2017-07-31
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5 Easy Steps to PDB Deposition (wwPDB News)
2017-06-07 (last edited: 6 months ago)2017-07-31
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Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive (wwPDB News)
2017-05-19 (last edited: 6 months ago)2017-07-31
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Enriched PDB Structure Entry Files Conforming to OneDep Data Standards Are Now Available for Testing (wwPDB News)
2017-05-03 (last edited: 6 months ago)2017-07-31
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Freezing the PDB Format (wwPDB News)
2017-04-27 (last edited: 6 months ago)2017-07-31
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The schema of the PDBj Mine 2 RDB was upgraded to pdbx-v42-v4.069.

On 2017-04-19 the schema of the PDBj Mine 2 RDB was upgraded to pdbx-v42-v4.069, adding support for new tables such as pdbx_deposit_group, enabling searching for group deposition IDs either via the omni search, advanced search or the SQL search.

Similarly, the dump files of the RDB on the FTP have also been updated. In case you experience any issues updating your local RDB with the delta file, please use the full dump file to upgrade the RDB as described on the RDB help page.
2017-04-19 (last edited: 9 months ago)2017-04-19
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Archival PDBx/mmCIF Version V4 to V5 Update in the Protein Data Bank (wwPDB News)
2017-03-23
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Updated Validation Reports for Archived PDB Structures Now Available (wwPDB News)
2017-03-16 (last edited: 10 months ago)2017-03-17
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Data Management: A global coalition to sustain core data (wwPDB News)
2017-03-15 (last edited: 10 months ago)2017-03-15
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The paper describing wwPDB OneDep system is now available (wwPDB News)
2017-02-10
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Time-stamped Copies of the PDB Archive Available (wwPDB News)
2017-01-12
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